3UBP | pdb_00003ubp

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UBP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3		WELL SOLUTIONS: 1.9 M AMMONIUM SULPHATE, 4MM PHENYLPHOSPHORODIAMIDATE, 1OOMM SODIUM CITRATE PH 6.3. PROTEIN SOLUTION: 20 C, 3 MICROLITERS PROTEIN SOLUTION ( 11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM PHENYLPHOSPHORODIAMIDATE) + 3 MICROLITERS PRECIPITANT SOLUTION, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.532	α = 90
b = 131.532	β = 90
c = 188.451	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	IMAGE PLATE	MARRESEARCH	BENT MIRROR	1997-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A		EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2	20	99.9	0.15	0.15	9.72	13.38		65301		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.04	99.9		0.536	0.536	2.8	7.56

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	RFREE	2UBP	2	18	65301	1306	99.9	0.158	0.158	0.16	0.2	RANDOM	15.87

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	30.5
p_staggered_tor	15
p_planar_tor	5.9
p_scangle_it	4.634
p_scbond_it	3.855
p_mcangle_it	2.077
p_mcbond_it	1.648
p_multtor_nbd	0.25
p_singtor_nbd	0.183
p_planar_d	0.033
p_angle_d	0.028
p_bond_d	0.009
p_angle_deg
p_hb_or_metal_coord
p_plane_restr
p_chiral_restr
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6055
Nucleic Acid Atoms
Solvent Atoms	841
Heterogen Atoms	7

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling