7B58 | pdb_00007b58

X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Cl determined at 1.72 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
2.76	55.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.441	α = 90
b = 131.441	β = 90
c = 189.759	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	1.72	189.76	100	0.134	0.141	0.044	1	19.3	19.6		102636			27.5

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	1.72	1.75	99.9		4.03	4.235	1.297	0.699	1	20.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G48	1.72	72.989	102502	5112	99.904	0.157	0.1555	0.17	0.1852	0.2	random	31.389

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]
1.082	0.541		1.082		-3.511

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.301
r_dihedral_angle_4_deg	17.41
r_dihedral_angle_3_deg	13.371
r_lrange_it	7.82
r_lrange_other	7.454
r_dihedral_angle_1_deg	7.359
r_scangle_it	5.429
r_scangle_other	4.622
r_scbond_it	3.827
r_scbond_other	3.323
r_mcangle_it	2.649
r_mcangle_other	2.649
r_mcbond_it	2.184
r_mcbond_other	2.182
r_angle_refined_deg	1.708
r_angle_other_deg	1.424
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.186
r_nbd_other	0.183
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6047
Nucleic Acid Atoms
Solvent Atoms	621
Heterogen Atoms	150

Software

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