2BSL | pdb_00002bsl

Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,4-dihydroxybenzoate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5		17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.62	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.588	α = 90
b = 108.16	β = 104.06
c = 66.222	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	MARRESEEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	2.3	25	90.6	0.06	22.9	5.7		32557		-3	26

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	2.3	2.32	62.8		0.23	5.6

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	PDB ENTRY 1OVD	2.3	25	27913	1526	90.6	0.189	0.186	0.19	0.241	0.24	RANDOM	36.13

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]
6.63		-0.68	-4.28		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.047
r_scangle_it	3.778
r_scbond_it	2.294
r_angle_refined_deg	1.687
r_mcangle_it	1.505
r_angle_other_deg	0.925
r_mcbond_it	0.809
r_nbd_other	0.234
r_nbd_refined	0.216
r_symmetry_vdw_other	0.215
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.1
r_nbtor_other	0.088
r_symmetry_hbond_refined	0.066
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4818
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	85

Software

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