X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details PEG 4000 (25%-29%), 0.1 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.34 α = 90
b = 57.34 β = 90
c = 264.75 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 97
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-05-01
Diffraction Radiation
Monochromator Protocol
diamond (111), germanium (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2

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
2.49 20 82.4 0.053 -- -- -- 15216 15053 0.0 0.0 31.4
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)
2.49 2.58 78.0 0.119 -- 4.7 -- 1376

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 2.49 19.33 -- 0.0 15016 15016 1184 92.5 0.218 0.214 0.214 0.264 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 2.49 2.66 -- 180 2095 0.28 0.314 0.023 87.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.8
Anisotropic B[1][1] -3.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.75
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 8.66
c_scbond_it 6.02
c_mcangle_it 10.22
c_mcbond_it 7.75
c_improper_angle_d 1.54
c_bond_d 0.012
c_angle_deg 1.4
c_dihedral_angle_d 24.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3352
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 232

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement