4AC7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S3T	PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.3		1.8 M AMMONIUM SULPHATE, 100 MM CITRATE PH 6.3, 50 MM NA2SO3

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.555	α = 90
b = 131.555	β = 90
c = 189.521	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	CCD	MARRESEARCH		2011-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)		PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	113.93	99.9	0.1	22.6	15.5		153738		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	100		0.58	4	9.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING	1.5	113.93	145792	7712	99.86	0.11847	0.11703	0.14605	RANDOM	13.109

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]
0.52	0.26		0.52		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.847
r_sphericity_free	24.641
r_dihedral_angle_4_deg	16.322
r_dihedral_angle_3_deg	11.53
r_sphericity_bonded	7.086
r_dihedral_angle_1_deg	6.259
r_rigid_bond_restr	2.383
r_angle_refined_deg	1.448
r_angle_other_deg	0.947
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6014
Nucleic Acid Atoms
Solvent Atoms	671
Heterogen Atoms	76

Software

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