X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 8.5
Temperature 287.0
Details Dihydrogen Phosphate, Tris-Hcl, pH 8.5, microbatch, temperature 287K
Method Microbatch
pH 4.6
Temperature 287.0
Details Ammonium Sulphate, Sodium acetate, pH 4.6, microbatch, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72 α = 90
b = 133.94 β = 90
c = 73.25 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirrors 2001-03-31
Diffraction Radiation
Monochromator Protocol
Sagitally focused Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1

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
2.3 29.34 91.9 0.04 0.034 -- 3.6 35212 31239 2.0 2.0 43.4
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)
2.3 2.42 90.5 0.2 0.17 3.6 3.2 4787

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
Single Wavelength Anomalous Dispersion 2.3 29.34 -- 0.0 31239 31239 1518 95.0 0.242 0.242 0.238 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 2.3 2.44 4787 236 4551 0.268 0.302 0.02 90.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 55.7
Anisotropic B[1][1] 13.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.17
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.63
c_scbond_it 2.68
c_mcangle_it 2.79
c_mcbond_it 1.65
c_improper_angle_d 0.65
c_dihedral_angle_d 21.1
c_angle_deg 1.0
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3738
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 220

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
Solve/Resolve model building