X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 2.3M Na-bicine pH 9, 2.3M Na-malonate pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.02 α = 90
b = 40.96 β = 104.08
c = 71.74 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR555 FLAT PANEL Detector swing-out angle up to 30 degrees 2010-11-14
Diffraction Radiation
Monochromator Protocol
Si (111), horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8174 EMBL/DESY, Hamburg X11

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
1.75 30.36 99.0 0.058 0.058 -- 7.2 -- 23825 -- -- 18.8
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)
1.75 1.84 98.6 0.266 0.266 2.4 7.3 3435

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
MR 1.75 28.89 0.0 0.0 -- 23812 2419 -- 0.182 0.182 0.182 0.229 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 1.75 1.795 1569 173 -- 0.285 0.329 0.138 98.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.632
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.104
r_dihedral_angle_1_deg 6.658
r_dihedral_angle_2_deg 34.888
r_bond_refined_d 0.015
r_angle_refined_deg 1.487
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 195

Software

Software
Software Name Purpose
REFMAC refinement
MOSFLM data reduction
SCALA data scaling version: 3.2.19
PDB_EXTRACT data extraction version: 3.006