9R32 | pdb_00009r32

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ELO

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	Protein: 30 mg/ml in 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM TCEP, pH 7 Reservoir: 25% PEG 3350, 0.1 M tris pH 7.8, 0.2 M Li sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.48

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+		2019-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5417

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	142.76	97.3	0.093	0.055	0.997	11.8	6.9		187306			18.767

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	90		0.658	0.514	0.706

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	1.9	91.768	187254	9337	97.166	0.181	0.1802	0.1886	0.2064	0.2118	21.331

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]
-0.439		-0.495	1.227		-0.783

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.82
r_dihedral_angle_3_deg	12.113
r_dihedral_angle_2_deg	8.445
r_dihedral_angle_1_deg	6.82
r_lrange_it	5.613
r_lrange_other	5.558
r_scangle_it	4.493
r_scangle_other	4.491
r_scbond_it	2.87
r_scbond_other	2.866

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.82
r_dihedral_angle_3_deg	12.113
r_dihedral_angle_2_deg	8.445
r_dihedral_angle_1_deg	6.82
r_lrange_it	5.613
r_lrange_other	5.558
r_scangle_it	4.493
r_scangle_other	4.491
r_scbond_it	2.87
r_scbond_other	2.866
r_mcangle_it	2.641
r_mcangle_other	2.64
r_mcbond_it	1.851
r_mcbond_other	1.85
r_angle_refined_deg	1.543
r_angle_other_deg	0.522
r_nbd_refined	0.209
r_nbd_other	0.197
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.066
r_ncsr_local_group_4	0.057
r_ncsr_local_group_6	0.057
r_ncsr_local_group_3	0.053
r_ncsr_local_group_1	0.045
r_ncsr_local_group_2	0.045
r_ncsr_local_group_5	0.039
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16196
Nucleic Acid Atoms
Solvent Atoms	1376
Heterogen Atoms	255

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.