Experiment: 9P62

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A8Z

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	1.2 M NaCl and 100 mM AcONa pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.05

Symmetry
Space Group	P 43 21 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	PIXEL	Bruker PHOTON II		2024-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	1.54184

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.499	25.056	99	0.99	18	1		19730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4999	25.056			0.99

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	FREE R-VALUE	1.499	25.056	19730	955	98.419	0.265	0.2627	0.2693	0.3224	0.3266	17.838

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]
0.008			0.008		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.79
r_lrange_it	13.605
r_lrange_other	13.594
r_dihedral_angle_3_deg	11.525
r_dihedral_angle_2_deg	8.827
r_dihedral_angle_1_deg	6.818
r_scangle_it	3.991
r_scangle_other	3.988
r_scbond_it	2.565
r_scbond_other	2.563

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.79
r_lrange_it	13.605
r_lrange_other	13.594
r_dihedral_angle_3_deg	11.525
r_dihedral_angle_2_deg	8.827
r_dihedral_angle_1_deg	6.818
r_scangle_it	3.991
r_scangle_other	3.988
r_scbond_it	2.565
r_scbond_other	2.563
r_mcangle_other	2.377
r_mcangle_it	2.37
r_angle_refined_deg	1.702
r_mcbond_it	1.575
r_mcbond_other	1.569
r_angle_other_deg	0.634
r_symmetry_nbd_refined	0.421
r_xyhbond_nbd_refined	0.418
r_nbd_refined	0.377
r_symmetry_xyhbond_nbd_refined	0.356
r_symmetry_nbd_other	0.309
r_nbd_other	0.283
r_nbtor_refined	0.182
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.061
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	20

Software
Software Name	Purpose
REFMAC	refinement

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.

9P62 | pdb_00009p62