X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 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 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 # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1998-01-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU/MSC RU-H2R -- -- --

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
2.48 22.9 93.6 -- 0.106 -- 2.6 -- 16723 -- -3.0 --
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)
2.48 2.59 82.1 -- 0.46 2.7 2.2 --

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 2.48 22.9 -- 0.0 -- 16723 797 93.6 -- 0.205 0.205 0.296 RANDOM, USING XPLOR
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 2.48 2.59 -- 97 1817 0.353 0.428 -- 82.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.1
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.35
x_scbond_it 3.84
x_mcangle_it 5.35
x_mcbond_it 3.84
x_improper_angle_d 0.97
x_bond_d 0.006
x_angle_deg 1.29
x_dihedral_angle_d 22.2
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 22.9
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3840
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 131

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.851 model building