4I1I | pdb_00004i1i

Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H7P	PDB ENTRY 4H7P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	290	EmeraldBio PACT screen a3: 25% PEG 1500, 100mM SPG buffer pH 6.0; LemaA.01212.a.A1.P001468 at 15mg/ml + 2.5mM NAD, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.82	α = 90
b = 65.13	β = 110.67
c = 77.49	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 225 mm CCD		2012-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.5	50	99.2	0.059	12.27	3.7	96750	95941		-3	25.149

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	94.2		0.35	0.35	2.78	2.6	7124

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4H7P	1.5	48.5	96750	95920	4794	99.26	0.1459	0.1459	0.1449	0.1441	0.1655	0.1649	RANDOM	21.1806

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]
0.09		0.07	0.1		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_4_deg	14.204
r_dihedral_angle_3_deg	11.232
r_dihedral_angle_1_deg	6.367
r_mcangle_it	1.84
r_angle_refined_deg	1.664
r_mcbond_it	1.189
r_mcbond_other	1.189
r_angle_other_deg	0.803
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_4_deg	14.204
r_dihedral_angle_3_deg	11.232
r_dihedral_angle_1_deg	6.367
r_mcangle_it	1.84
r_angle_refined_deg	1.664
r_mcbond_it	1.189
r_mcbond_other	1.189
r_angle_other_deg	0.803
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4567
Nucleic Acid Atoms
Solvent Atoms	623
Heterogen Atoms	79

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.