X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 8000, calcium acetate, sodium acetate, imidazole, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.13 α = 90
b = 132.07 β = 108.14
c = 80.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-11-17
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.00 SPring-8 BL44B2

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
2.2 20 96.8 0.046 0.046 -- 3.1 76595 76595 0.0 0.0 16.994
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)
2.2 2.24 91.5 0.125 0.125 2.673 2.4 3601

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 2.2 20.0 0.0 0.0 76592 68913 7679 96.5 0.212 0.212 0.207 0.253 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 2.2 2.28 -- 755 6511 0.2268 0.2875 -- 91.95
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 36.4512
Anisotropic B[1][1] -5.755
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.677
Anisotropic B[2][2] 6.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.715
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_dihedral_angle_d 21.302
c_angle_deg 1.18733
c_improper_angle_d 0.81863
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11973
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 309

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement
DENZO data reduction
SCALEPACK data scaling