2ORM | pdb_00002orm

Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BJP	PDB ENTRY 1BJP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees Celcius against 50 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.83	α = 90
b = 50.77	β = 99.13
c = 89.31	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	108	IMAGE PLATE	RIGAKU RAXIS IV		2000-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	24.5	90	0.096	13.5	5.94		20368			19.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	90		0.476	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	RANDOM	PDB ENTRY 1BJP	2.1	24.5	21823	20368	1044	92.1	0.217	0.217	0.22	0.249	0.25	THROUGHOUT	31

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]
1.99		0.85	-2.06		0.07

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.5
c_angle_deg	1.1
c_improper_angle_d	0.77
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2932
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling