6ZO2 | pdb_00006zo2

1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-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	55.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.64	α = 90
b = 131.64	β = 90
c = 189.254	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 EIGER X 4M		2018-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.96769	ESRF	ID30B

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	1.65	62.245	100	0.131	0.137	0.042	0.999	18.6	20.5		116041			20.6

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	1.65	1.68	100		2.811	2.947	0.883	0.771	1.5	21.2

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	1.65	62.24	115979	5813	99.974	0.136	0.1344	0.15	0.1556	0.17	24.979

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]
0.729	0.365		0.729		-2.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.325
r_dihedral_angle_4_deg	17.885
r_dihedral_angle_3_deg	12.236
r_dihedral_angle_1_deg	7.018
r_lrange_it	6.338
r_lrange_other	6.338
r_scangle_it	4.819
r_scangle_other	4.403
r_scbond_it	3.261
r_scbond_other	3.015
r_mcangle_it	2.278
r_mcangle_other	2.278
r_angle_refined_deg	1.745
r_mcbond_it	1.666
r_mcbond_other	1.664
r_angle_other_deg	1.475
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.211
r_nbd_other	0.206
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.137
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.012
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	648
Heterogen Atoms	170

Software

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