8A18 | pdb_00008a18

1.63 A resolution hydroquinone inhibited Sporosarcina pasteurii urease

X-RAY DIFFRACTION

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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	6.5	293	THE PROTEIN-LIGAND (1 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50, DILUTED 1:1 WITH A SOLUTION OF 1.6-2.0 M AMMONIUM SULFATE in 100 mM citrate buffer at pH 6.3

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.666	α = 90
b = 131.666	β = 90
c = 189.129	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-F		2022-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9537	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.63	115	100	0.12	0.127	0.043	19.9	16.3		120118

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66	100		1.99	2.142	0.786	1.5	14.1

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	1.63	114.287	120090	5968	99.864	0.129	0.1279	0.14	0.158	0.17	22.827

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]
0.68	0.34		0.68		-2.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.016
r_dihedral_angle_4_deg	18.179
r_dihedral_angle_3_deg	12.492
r_dihedral_angle_other_3_deg	11.858
r_lrange_it	7.294
r_lrange_other	7.151
r_dihedral_angle_1_deg	6.92
r_scangle_it	4.886
r_scangle_other	4.487
r_scbond_it	3.392
r_scbond_other	3.059
r_mcangle_other	2.297
r_mcangle_it	2.296
r_angle_refined_deg	1.851
r_mcbond_it	1.685
r_mcbond_other	1.682
r_angle_other_deg	1.5
r_nbd_refined	0.237
r_nbd_other	0.226
r_symmetry_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.163
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.077
r_xyhbond_nbd_other	0.035
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6046
Nucleic Acid Atoms
Solvent Atoms	667
Heterogen Atoms	184

Software

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