9DMC | pdb_00009dmc

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9BPY

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.54

Symmetry
Space Group	P 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2024-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18	CLSI	08B1-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3	29.77	93.9	0.062	0.072	0.037	0.998	15.1	3.6		18710

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.18		86	0.578	0.683	0.356	0.918		3.4

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3	25	17490	918	92.38	0.29363	0.29249	0.2773	0.31655	0.3041	RANDOM	109.948

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-5.68	6.84	-2.27	13.26	2.05	-10.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.232
r_dihedral_angle_1_deg	6.666
r_long_range_B_refined	5.859
r_long_range_B_other	5.858
r_dihedral_angle_2_deg	5.515
r_mcangle_it	3.581
r_mcangle_other	3.581
r_scangle_other	2.899
r_mcbond_it	2.048
r_mcbond_other	2.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.232
r_dihedral_angle_1_deg	6.666
r_long_range_B_refined	5.859
r_long_range_B_other	5.858
r_dihedral_angle_2_deg	5.515
r_mcangle_it	3.581
r_mcangle_other	3.581
r_scangle_other	2.899
r_mcbond_it	2.048
r_mcbond_other	2.047
r_scbond_it	1.565
r_scbond_other	1.563
r_angle_refined_deg	0.921
r_angle_other_deg	0.316
r_chiral_restr	0.041
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded