1E7Y | pdb_00001e7y

ACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES COMPLEXED WITH SUBSTRATE AND NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		REFINED COORDINATES OF APO-ENZYME IN THE SAME SPACEGROUP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. IN THE WELL BUFFER: 14% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 15MG/ML, WITH 2.3MM GLUCOSE 6-PHOSPHATE AND 0.6MM NADPH.

Crystal Properties
Matthews coefficient	Solvent content
2.3	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129	α = 90
b = 44	β = 105.2
c = 91.1	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	IMAGE PLATE	MARRESEARCH	MIRRORS	1998-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.48	22.9	93.6	0.106	9	2.6		16723		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.48	2.59	82.1		0.46	2.7	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	FREE R-VALUE	REFINED COORDINATES OF APO-ENZYME IN THE SAME SPACEGROUP	2.48	22.9	16723	797	93.6	0.205	0.205	0.2	0.296	0.28	RANDOM, USING XPLOR	30.1

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
x_dihedral_angle_d	22.2
x_mcangle_it	5.35
x_scangle_it	5.35
x_mcbond_it	3.84
x_scbond_it	3.84
x_angle_deg	1.29
x_improper_angle_d	0.97
x_bond_d	0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3840
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	44

Software

Software
Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing