2BX7 | pdb_00002bx7

Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,5-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	8.8		HANGING DROPS OF 2 MICROLITERS PROTEIN AND INHIBITOR (17 MG/ML PROTEIN AND 2.6 MM 3, 5-DIHYDROXYBENZOATE) AND 2 MIKROLITERS RESERVOIR. DROPS WERE EQUILIBRATED OVER 1 ML RESERVOIR SOLUTION. RESERVOIR SOLUTION: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL, PH 8.8

Crystal Properties
Matthews coefficient	Solvent content
2.57	51.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.71	α = 90
b = 108.127	β = 104.06
c = 66.216	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	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	2.03	25	93.1	0.08	21.5	3.9		47526

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	2.03	2.08	47.5		0.34	6.3

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	2.04	25	41966	2236	94.8	0.187	0.184	0.19	0.229	0.23	RANDOM	28.46

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]
3.76		-0.52	-2.42		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.571
r_scangle_it	3.839
r_scbond_it	2.377
r_mcangle_it	1.561
r_angle_refined_deg	1.528
r_angle_other_deg	0.882
r_mcbond_it	0.843
r_nbd_other	0.237
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.2
r_symmetry_vdw_other	0.164
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.095
r_nbtor_other	0.084
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
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	275
Heterogen Atoms	85

Software

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