9XYW | pdb_00009xyw

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GQ2

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	8% w/v PEG20000, 8% w/v PEG550 MME, 50 mM Tris-HCl, pH 8.5, 1.2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.29

Symmetry
Space Group	P 21 2 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	DECTRIS EIGER X 16M		2024-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.55	91.232	99.9	0.112	0.122	0.049	0.998	9.7	6		55927			65

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	2.55	2.62	100		1.832	2.003	0.803	0.603	1	6.2

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-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	2.55	91.232	55877	2736	99.846	0.247	0.2467	0.2435	0.256	0.3083	0.3225	RANDOM	103

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]
-3.608			11.419		-7.811

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.551
r_dihedral_angle_3_deg	20.696
r_dihedral_angle_4_deg	19.643
r_lrange_it	17.728
r_lrange_other	17.727
r_mcangle_it	13.688
r_mcangle_other	13.687
r_scangle_it	12.614
r_scangle_other	12.613
r_mcbond_it	9.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.551
r_dihedral_angle_3_deg	20.696
r_dihedral_angle_4_deg	19.643
r_lrange_it	17.728
r_lrange_other	17.727
r_mcangle_it	13.688
r_mcangle_other	13.687
r_scangle_it	12.614
r_scangle_other	12.613
r_mcbond_it	9.107
r_mcbond_other	9.106
r_scbond_it	8.061
r_scbond_other	8.06
r_dihedral_angle_1_deg	8.016
r_angle_refined_deg	1.753
r_angle_other_deg	1.214
r_nbd_other	0.275
r_nbd_refined	0.244
r_symmetry_nbd_refined	0.218
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.161
r_ncsr_local_group_1	0.16
r_metal_ion_refined	0.102
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8316
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	116

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.