4E0B | pdb_00004e0b

2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HHP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	295	Protein: 3.3 mg/mL. Crystallization conditions: 30%PEG 8K, 0.2M Na Acetate , 0.1M Bis-Tris pH 7.0. , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.04	α = 90
b = 80.76	β = 109.42
c = 99.43	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	100	CCD	MARMOSAIC 300 mm CCD	BE-LENSES	2012-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G		APS	21-ID-G

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	2.17	30	99.9	0.114	13.87	5.3		62995		-3

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	2.17	2.21	99.9		0.679	2.19	4.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	3HHP	2.17	29.2	59311	59311	3147	99.8	0.165	0.163	0.18	0.207	0.21	RANDOM	34.21

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]
1.34		-0.74	-0.64		-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.108
r_dihedral_angle_4_deg	8.748
r_dihedral_angle_3_deg	7.607
r_scangle_it	2.719
r_dihedral_angle_1_deg	1.645
r_scbond_it	1.629
r_angle_refined_deg	1.27
r_mcangle_it	0.91
r_angle_other_deg	0.796
r_mcbond_it	0.487
r_mcbond_other	0.109
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8875
Nucleic Acid Atoms
Solvent Atoms	709
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Blu-Ice	data collection
mrbump/molrep	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MRBUMP/MOLREP	phasing