6ZNY | pdb_00006zny

1.50 A resolution 3-methylcatechol (3-methylbenzene-1,2-diol) 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	6.3	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
2.77	55.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.577	α = 90
b = 131.577	β = 90
c = 189.365	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		2016-07-13	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)	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	1.5	113.949	99.7	0.113	0.121	0.042	0.999	18.8	15.4		153039			15.9

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	1.5	1.53	99.1		2.359	2.526	0.9	0.687	1.5	14.9

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	1.5	94.862	153002	7683	99.572	0.134	0.133	0.13	0.1521	0.15	21.148

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]
0.742	0.371		0.742		-2.406

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.393
r_dihedral_angle_4_deg	18.228
r_dihedral_angle_3_deg	12.308
r_dihedral_angle_1_deg	6.959
r_lrange_it	5.443
r_lrange_other	5.259
r_scangle_it	4.315
r_scangle_other	4.174
r_scbond_it	2.961
r_scbond_other	2.846
r_mcangle_other	2.071
r_mcangle_it	2.07
r_angle_refined_deg	1.755
r_angle_other_deg	1.491
r_mcbond_it	1.462
r_mcbond_other	1.46
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.2
r_nbd_other	0.187
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.158
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6041
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	169

Software

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