X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.7
Temperature 277.0
Details 2-methyl-2,4-pentanediol, HEPES buffer, guanidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.72 α = 90
b = 59.72 β = 90
c = 209.96 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-05-16
CCD ADSC QUANTUM 4 -- 2001-05-12
Diffraction Radiation
Monochromator Protocol
double crystal monochromator MAD
Flat mirror (vFlat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.978996, 0.904964 SSRL BL9-2
SYNCHROTRON SSRL BEAMLINE BL11-1 0.964818 SSRL BL11-1

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 22.72 95.6 -- 0.042 -- 6.6 26060 25218 1.0 -- 21.8
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)
2.0 2.03 98.8 -- 0.135 -- 7.0 1263

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
MAD 2.0 22.72 -- 1.0 48653 46739 4568 95.6 -- 0.237 0.237 0.26 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 2.0 2.13 -- 741 6689 0.245 0.285 0.01 90.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 37.0
Anisotropic B[1][1] 5.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.49
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.07
c_scbond_it 2.24
c_mcangle_it 1.91
c_mcbond_it 1.21
c_improper_angle_d 6.24
c_bond_d 0.25
c_angle_deg 5.1
c_dihedral_angle_d 26.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2069
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 87

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS 1.1 Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS version: 1.1 model building