Experiment: 9WM4

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8WIP	Pseudomonas aeruginosa SuhB apo form

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	Sodium acetate trihydrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

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	IMAGE PLATE	MAR scanner 345 mm plate		2024-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97893	RRCAT INDUS-2	PX-BL21

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	2.4	48.27	100	0.093	0.102	0.043	0.998	15.4	5.7		20413

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	2.4	2.53	100		0.578	0.636	0.263	0.856	3.3	5.7

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	2.4	48.27	19287	1078	99.96	0.1809	0.17804	0.1829	0.232	0.226	RANDOM	41.996

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]
2.76			-2.13		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.485
r_dihedral_angle_2_deg	7.712
r_long_range_B_refined	7.55
r_long_range_B_other	7.414
r_dihedral_angle_1_deg	6.746
r_scangle_other	5.244
r_mcangle_it	4.321
r_mcangle_other	4.32
r_scbond_it	3.197
r_scbond_other	3.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.485
r_dihedral_angle_2_deg	7.712
r_long_range_B_refined	7.55
r_long_range_B_other	7.414
r_dihedral_angle_1_deg	6.746
r_scangle_other	5.244
r_mcangle_it	4.321
r_mcangle_other	4.32
r_scbond_it	3.197
r_scbond_other	3.171
r_mcbond_it	2.646
r_mcbond_other	2.645
r_angle_refined_deg	1.624
r_angle_other_deg	0.56
r_chiral_restr	0.078
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4019
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	14

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.

9WM4 | pdb_00009wm4