3P4Q | pdb_00003p4q

Crystal structure of Menaquinol:oxidoreductase in complex with oxaloacetate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.8	298	12.5% PEG 5000 mme, 85mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, 5mM fumarate, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.641	α = 90
b = 137.964	β = 90
c = 272.803	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0	SSRL	BL9-2

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	3.35	50	88.9	0.099	10.2	3.1		47456

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)
	3.35	3.47	73.9		0.237		2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	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)	Mean Isotropic B
X-RAY DIFFRACTION		3.35	47.57	47428	920	89.2	0.221	0.22	0.2194	0.261	0.2573	95.455

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]
-0.11			-3.1		3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.661
r_dihedral_angle_3_deg	17.4
r_dihedral_angle_4_deg	15.539
r_dihedral_angle_1_deg	4.973
r_angle_refined_deg	1.868
r_scangle_it	0.839
r_mcangle_it	0.518
r_scbond_it	0.468
r_chiral_restr	0.449
r_mcbond_it	0.281
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16642
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	162

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction