7B5A | pdb_00007b5a

X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)2NO3 determined at 1.97 Angstroms

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6G48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.485	α = 90
b = 131.485	β = 90
c = 189.523	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		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	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)	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	1.97	113.87	100	0.2	0.234	0.064	0.998	12.2	13.2		68762			29.2

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	1.97	2.02	99.9		3.191	3.473	0.982	0.593	1	12.4

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	6G48	1.97	97.798	68710	3343	99.953	0.169	0.1668	0.18	0.2092	0.22	37.581

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]
1.569	0.784		1.569		-5.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.793
r_dihedral_angle_4_deg	17.73
r_dihedral_angle_3_deg	14.512
r_dihedral_angle_1_deg	7.705
r_lrange_it	6.794
r_lrange_other	6.685
r_scangle_it	5.736
r_scangle_other	5.283
r_scbond_it	4.111
r_scbond_other	3.819
r_mcangle_it	3.664
r_mcangle_other	3.664
r_mcbond_it	2.882
r_mcbond_other	2.881
r_angle_refined_deg	1.756
r_angle_other_deg	1.386
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.206
r_nbd_other	0.196
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_other	0.116
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6047
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	107

Software

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