6RP1 | pdb_00006rp1

1.49 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 6.5

X-RAY DIFFRACTION

---

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	Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.813	α = 90
b = 131.813	β = 90
c = 189.028	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		2018-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9797	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	1.49	114.15	99.8	0.123	0.133	0.036	0.999	15.3	13.2		156618			13.3

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	1.49	1.52	99.4		1.933	2.115	0.607	0.575	1.5	11.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5OL4	1.49	114.15	148730	7859	99.74	0.13702	0.13619	0.14	0.15302	0.15	RANDOM	19.406

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]
0.54	0.27		0.54		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.392
r_dihedral_angle_4_deg	17.889
r_dihedral_angle_3_deg	11.749
r_dihedral_angle_1_deg	6.047
r_long_range_B_refined	5.307
r_long_range_B_other	5.306
r_scangle_other	2.941
r_scbond_it	1.878
r_scbond_other	1.878
r_mcangle_it	1.532
r_mcangle_other	1.532
r_angle_refined_deg	1.442
r_mcbond_it	0.991
r_mcbond_other	0.989
r_angle_other_deg	0.8
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6046
Nucleic Acid Atoms
Solvent Atoms	709
Heterogen Atoms	97

Software

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