X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.8
Details HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE PROTEIN AT 5MG/ML IN 100MM TRIS-HCL AT PH 7.5 WITH 0.5MM NADP+. DROPS EQUILIBRIATED AGAINST 1.7M UNBUFFERED AMMONIUM SULFATE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.7 α = 90
b = 136.7 β = 90
c = 121.2 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1994-11-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.16 25 90.2 -- 0.138 -- 2.8 -- 32868 -- -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)
2.16 2.24 81.3 -- 0.506 1.8 2.5 --

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 2.16 21.2 -- 0.0 -- 32685 2572 90.1 -- 0.187 0.187 0.226 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 2.16 2.24 -- 216 2606 0.316 0.323 -- 81.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.3
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.48
x_scbond_it 2.58
x_mcangle_it 3.48
x_mcbond_it 2.58
x_improper_angle_d 1.01
x_bond_d 0.006
x_angle_deg 1.264
x_dihedral_angle_d 22.53
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 21.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3837
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 191

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.1 model building