9V9D | pdb_00009v9d

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WPI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.05 M Lithium acetate, 0.1 M HEPES 7.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.96

Symmetry
Space Group	P 21 21 21

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	RIGAKU HyPix-6000HE		2025-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	26.981	99.9	0.16	12.3	9		16849

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59			0.39	5.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.501	26.981	16787	828	99.845	0.231	0.2297	0.2322	0.257	0.2627	16.49

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]
-1.807			-0.073		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.198
r_dihedral_angle_3_deg	16.548
r_dihedral_angle_4_deg	15.689
r_dihedral_angle_1_deg	5.74
r_angle_other_deg	2.319
r_lrange_it	1.479
r_lrange_other	1.452
r_angle_refined_deg	1.182
r_mcangle_it	0.499
r_mcangle_other	0.499

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.198
r_dihedral_angle_3_deg	16.548
r_dihedral_angle_4_deg	15.689
r_dihedral_angle_1_deg	5.74
r_angle_other_deg	2.319
r_lrange_it	1.479
r_lrange_other	1.452
r_angle_refined_deg	1.182
r_mcangle_it	0.499
r_mcangle_other	0.499
r_mcbond_it	0.263
r_mcbond_other	0.263
r_scangle_it	0.259
r_scangle_other	0.259
r_nbd_other	0.237
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.201
r_nbd_refined	0.163
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.128
r_scbond_it	0.124
r_scbond_other	0.124
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_xyhbond_nbd_other	0.067
r_symmetry_nbtor_other	0.065
r_chiral_restr	0.043
r_bond_other_d	0.035
r_gen_planes_other	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4054
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	33

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.