1M67

Crystal Structure of Leishmania mexicana GPDH Complexed with Inhibitor 2-bromo-6-hydroxy-purine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	298	NaCitrate, TEA, DTT, EDTA, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.503	α = 90
b = 70.503	β = 90
c = 211.738	γ = 90

Symmetry
Space Group	P 41 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	125	CCD	ADSC QUANTUM 4		2001-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.91942	APS	19-ID

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	2.5	50	98.9	0.089	34.4	15.4	19175	19175

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	2.5	2.56	98.9		0.62	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.5	50	19165	19165	983	98.9	0.2461	0.24399	0.24399	0.28606	RANDOM	48.892

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]
1.7			1.7		-3.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.185
r_scangle_it	4.042
r_dihedral_angle_1_deg	3.239
r_scbond_it	2.614
r_mcangle_it	2.015
r_angle_refined_deg	1.334
r_mcbond_it	1.06
r_symmetry_hbond_refined	0.512
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.185
r_scangle_it	4.042
r_dihedral_angle_1_deg	3.239
r_scbond_it	2.614
r_mcangle_it	2.015
r_angle_refined_deg	1.334
r_mcbond_it	1.06
r_symmetry_hbond_refined	0.512
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2602
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	29

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.