X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.8
Details HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE WELL BUFFER: 21% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.8 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 7MG/ML, WITH 20MM GLUCOSE 6-PHOSPHATE AND 10MM BENZAMIDE ADENINE DINUCLEOTIDE (BAD).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.8 α = 90
b = 44.3 β = 105.1
c = 91.2 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 1996-10-22
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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
2.69 24.9 94.6 -- 0.112 -- 2.9 -- 13462 -- -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)
2.69 2.79 93.1 -- 0.331 3.3 -- --

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 2.69 25.0 -- 0.0 -- 13462 645 94.6 -- 0.18 0.18 0.285 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 2.69 2.79 -- 55 1212 0.26 0.332 -- 93.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.64
x_scbond_it 3.29
x_mcangle_it 4.64
x_mcbond_it 3.29
x_improper_angle_d 0.92
x_bond_d 0.006
x_angle_deg 1.24
x_dihedral_angle_d 22.9
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 25.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3837
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 108

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