2DFD

Crystal Structure of Human Malate Dehydrogenase Type 2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1M MMT, 30% PEG1000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.943	α = 90
b = 152.526	β = 90
c = 154.827	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	MARMOSAIC 225 mm CCD		2005-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99806	SLS	X10SA

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	1.9	6.01	100				112689

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	100

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MLD	1.9	6.01	106859	106859	5642	99.81	0.15774	0.15774	0.15583	0.19416	RANDOM	25.38

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]
-0.74			0.75		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.152
r_dihedral_angle_4_deg	14.651
r_dihedral_angle_3_deg	12.98
r_dihedral_angle_1_deg	5.936
r_scangle_it	2.99
r_scbond_it	2.072
r_angle_refined_deg	1.542
r_mcangle_it	1.16
r_angle_other_deg	0.987
r_mcbond_it	0.866
r_mcbond_other	0.245
r_nbd_refined	0.215
r_symmetry_vdw_other	0.201
r_symmetry_vdw_refined	0.192
r_nbd_other	0.187
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.088
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9160
Nucleic Acid Atoms
Solvent Atoms	799
Heterogen Atoms	254

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing