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 MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.37 α = 90
b = 83.37 β = 90
c = 139.02 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-12-10
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.000 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
2.5 40 99.5 0.045 0.045 -- 20.9 19313 19313 0.0 0.0 58.195
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)
2.5 2.59 99.8 0.216 0.216 -- -- --

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
MIR 2.5 30.0 0.0 0.0 19313 19313 940 99.5 0.2219 0.2219 0.2219 0.2599 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 2.5 2.59 -- 87 -- 0.3484 0.3931 -- 0.976
X Ray Diffraction 2.59 2.69 -- 104 -- 0.3204 0.344 -- 0.998
X Ray Diffraction 2.69 2.82 -- 86 -- 0.2793 0.3053 -- 0.9953
X Ray Diffraction 2.82 2.96 -- 97 -- 0.3077 0.3659 -- 0.9985
X Ray Diffraction 2.96 3.15 -- 85 -- 0.2693 0.3268 -- 0.999
X Ray Diffraction 3.15 3.39 -- 105 -- 0.2201 0.2568 -- 0.9985
X Ray Diffraction 3.39 3.73 -- 95 -- 0.2454 0.2872 -- 1.0
X Ray Diffraction 3.73 4.27 -- 97 -- 0.2013 0.2163 -- 1.0
X Ray Diffraction 4.27 5.38 -- 86 -- 0.1788 0.2383 -- 0.9994
X Ray Diffraction 5.38 30.0 -- 98 -- 0.1723 0.2027 -- 0.9896
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.8703
Anisotropic B[1][1] -5.82
Anisotropic B[1][2] -4.385
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.639
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.27355
c_angle_deg 1.07324
c_bond_d 0.005558
c_dihedral_angle_d 18.4205
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.39
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1066
Nucleic Acid Atoms 855
Heterogen Atoms 0
Solvent Atoms 98

Software

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