9VP7 | pdb_00009vp7

Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with pseudo substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AQ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	4% Tacsimate, 12% PEG3350, 4-8% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.49	53.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.84	α = 90
b = 97.685	β = 94.005
c = 70.449	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	RIGAKU HyPix-6000HE		2023-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.25	30.195	99.8	0.96	6	6.7		61443

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	100		0.917		7.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	30.195	61423	3091	99.698	0.223	0.2196	0.223	0.2863	0.2905	22.543

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]
-0.468		-0.846	1.276		-0.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.083
r_dihedral_angle_6_deg	14.673
r_dihedral_angle_2_deg	9.688
r_dihedral_angle_1_deg	7.101
r_lrange_it	5.907
r_lrange_other	5.846
r_scangle_it	3.617
r_scangle_other	3.616
r_mcangle_it	3.171
r_mcangle_other	3.171
r_scbond_it	2.181
r_scbond_other	2.181
r_mcbond_it	1.942
r_mcbond_other	1.942
r_angle_refined_deg	1.32
r_angle_other_deg	0.475
r_chiral_restr_other	0.313
r_symmetry_nbd_refined	0.228
r_nbd_other	0.226
r_nbd_refined	0.218
r_symmetry_nbd_other	0.21
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.17
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.064
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8040
Nucleic Acid Atoms
Solvent Atoms	724
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing