X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION; THEN SOAKED WITH 10 MM G6P AND 5 MM GLUCOSE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83 α = 90
b = 122 β = 92
c = 123 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1997-02
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 -- SSRL BL7-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
2.79 38 96.9 -- 0.055 -- 1.9 -- 113243 -- 0.0 62.4
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.8 2.9 88.0 -- 0.32 3.0 1.4 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.8 8.0 -- 2.0 -- 55607 5653 96.4 -- 0.2 0.2 0.27 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.8 2.97 -- 887 7856 0.308 0.386 0.013 91.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 44.0
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.007
x_angle_deg 1.2
x_mcbond_it 3.83
x_dihedral_angle_d 25.3
x_mcangle_it 5.97
x_scbond_it 6.07
x_scangle_it 9.38
x_improper_angle_d 0.55
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.44
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14066
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 142

Software

Software
Software Name Purpose
X-PLOR model building version: 3.851
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.851