4WLU | pdb_00004wlu

Crystal structure of L-malate and NAD bound MDH2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	288	0.1 M Na2HPO4:citric acid, 40% (v/v) polyethylene glycol 300, 10% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.982	α = 90
b = 152.14	β = 90
c = 155.035	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	100	CCD	ADSC QUANTUM 270		2014-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.14	30.79	99.8	55.5	13.6		74182

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.14	30.79	74182	3924	98.45	0.21757	0.21612	0.22	0.2442	0.25	RANDOM	35.076

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.33
r_dihedral_angle_3_deg	13.157
r_dihedral_angle_4_deg	11.944
r_dihedral_angle_1_deg	5.133
r_long_range_B_refined	2.937
r_long_range_B_other	2.922
r_scangle_other	1.703
r_mcangle_it	1.461
r_mcangle_other	1.461
r_scbond_it	0.998
r_scbond_other	0.998
r_angle_refined_deg	0.984
r_mcbond_it	0.87
r_mcbond_other	0.87
r_angle_other_deg	0.76
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9248
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	212

Software

Software
Software Name	Purpose
REFMAC	refinement