3GVI | pdb_00003gvi

Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GVH	pdb entry 3GVH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	JCSG+ SCREEN, H3: 25% PEG 3350, 100MM BISTRIS, BRABA.00005.A AT 28.5MG/ML, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.39	α = 90
b = 193.9	β = 90
c = 102.68	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	2.25	193.9	97.3	0.051	18.82	4.2	102350	99622		-3	28.89

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)
	2.25	2.31	83.7		0.152	5.6	2	7486

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	MR	THROUGHOUT	pdb entry 3GVH	2.25	193	99617	99617	5000	97.3	0.177	0.174	0.17	0.228	0.22	RANDOM	14.95

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]
0.49			0.67		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.254
r_dihedral_angle_4_deg	14.413
r_dihedral_angle_3_deg	14.105
r_dihedral_angle_1_deg	5.58
r_scangle_it	3.748
r_scbond_it	2.34
r_angle_refined_deg	1.525
r_mcangle_it	1.412
r_angle_other_deg	0.927
r_mcbond_it	0.756
r_mcbond_other	0.232
r_chiral_restr	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13710
Nucleic Acid Atoms
Solvent Atoms	1311
Heterogen Atoms	162

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling