6ZO3 | pdb_00006zo3

1.55 A resolution 3,6-dimethylcatechol (3,6-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
2.76	55.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.463	α = 90
b = 131.463	β = 90
c = 189.067	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	0.9677	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	1.55	48.77	99.9	0.127	0.135	0.046	0.999	17.8	16		139215			13.2

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	1.55	1.58	97.5		2.145	2.288	0.792	0.67	1.5	15.6

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	1.55	47.311	139006	6983	99.967	0.136	0.1355	0.15	0.156	0.17	20.213

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]
0.681	0.34		0.681		-2.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.199
r_dihedral_angle_4_deg	18.057
r_dihedral_angle_3_deg	12.389
r_dihedral_angle_1_deg	7.01
r_lrange_it	5.592
r_lrange_other	5.592
r_scangle_it	4.037
r_scangle_other	3.827
r_scbond_it	2.723
r_scbond_other	2.581
r_mcangle_it	1.943
r_mcangle_other	1.943
r_angle_refined_deg	1.765
r_angle_other_deg	1.507
r_mcbond_it	1.408
r_mcbond_other	1.408
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.223
r_nbd_other	0.207
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.105
r_symmetry_nbtor_other	0.097
r_chiral_restr	0.093
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	6034
Nucleic Acid Atoms
Solvent Atoms	758
Heterogen Atoms	136

Software

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