6ZO0 | pdb_00006zo0

2.23 A resolution 3,4-dimethylcatechol (3,4-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G4H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	50 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.501	α = 90
b = 131.501	β = 90
c = 188.71	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

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 PILATUS 6M		2020-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.000	ELETTRA	11.2C

Data Collection

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	2.23	188.71	100	0.271	0.299	0.125	0.995	9	10.7		47585			27.9

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	2.23	2.3	100		1.751	1.929	0.804	0.657	1.5	11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5G4H	2.23	113.883	47536	2279	99.971	0.164	0.1611	0.16	0.2162	0.22	34.357

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]
1.038	0.519		1.038		-3.368

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.16
r_dihedral_angle_4_deg	19.595
r_dihedral_angle_3_deg	16.035
r_lrange_it	9.216
r_dihedral_angle_1_deg	7.57
r_scangle_it	6.299
r_scbond_it	4.562
r_mcangle_it	3.808
r_mcbond_it	2.757
r_angle_refined_deg	1.861

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.16
r_dihedral_angle_4_deg	19.595
r_dihedral_angle_3_deg	16.035
r_lrange_it	9.216
r_dihedral_angle_1_deg	7.57
r_scangle_it	6.299
r_scbond_it	4.562
r_mcangle_it	3.808
r_mcbond_it	2.757
r_angle_refined_deg	1.861
r_nbtor_refined	0.317
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.122
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6041
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

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.