1JRC | pdb_00001jrc

The N67A mutant of Lactococcus lactis dihydroorotate dehydrogenase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DOR	Lactococcus lactis DHODA, PDB ID 2DOR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 6K, Na-acetate, TRIS-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.8	α = 90
b = 108.09	β = 103.89
c = 65.8	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	120	IMAGE PLATE	MARRESEARCH		1999-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.84690	EMBL/DESY, HAMBURG	BW7B

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	1.84	20	98.8	0.059	22.8	3.9	433016	62505			12.6

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)
	1.84	1.87	87.2		0.207	5.3		2705

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Lactococcus lactis DHODA, PDB ID 2DOR	1.8	20	61507	61507	6195		0.177	0.1598	0.22	0.1952	RANDOM	16.66

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	27.1
p_planar_tor	12.7
p_staggered_tor	12.3
p_multtor_nbd	0.246
p_xyhbond_nbd	0.183
p_singtor_nbd	0.179
p_planar_d	0.076
p_angle_d	0.032
p_bond_d	0.017
p_xhyhbond_nbd
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4816
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms	84

Software

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