7P7N | pdb_00007p7n

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 ANGSTROMS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OL4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	THE PROTEIN-LIGAND (1.2 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.2-1.7 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.645	α = 90
b = 131.645	β = 90
c = 189.2	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		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	1.8	114	100	0.142	0.154	0.042	0.999	17	13.2		89759			25.26

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	1.8	1.83	100		2.3	2.484	0.931	0.694	1.5	13.5

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	5ol4	1.8	72.907	89704	4419	99.975	0.156	0.155	0.16	0.1763	0.18	31.017

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]
1.002	0.501		1.002		-3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_rigid_bond_restr	21.785
r_dihedral_angle_4_deg	17.946
r_dihedral_angle_3_deg	14.048
r_lrange_it	7.792
r_dihedral_angle_1_deg	7.187
r_scangle_it	5.945
r_scbond_it	4.443
r_mcangle_it	3.033
r_mcbond_it	2.422
r_angle_refined_deg	1.747
r_nbtor_refined	0.308
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.198
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5994
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	143

Software

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