X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 4.0
Details Phosphate buffer, PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.71 α = 90.55
b = 49.07 β = 94.33
c = 53.12 γ = 90.31
Symmetry
Space Group P -1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC Yale mirrors 1994-10-10
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
1.8 25 87.2 0.046 -- -- -- 36070 31453 0.0 0.0 10.3
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)
1.8 1.83 41.8 0.289 -- 2.3 2.0 31453

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 1.9 6.0 -- 2.0 -- 22299 2178 74.9 -- -- 0.249 0.293 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 1.9 2.01 -- 264 2517 0.306 0.308 0.019 56.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.1
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.47
Anisotropic B[1][3] -0.48
Anisotropic B[2][2] 0.74
Anisotropic B[2][3] -0.67
Anisotropic B[3][3] -0.58
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.15
x_scbond_it 4.16
x_mcangle_it 4.7
x_mcbond_it 3.72
x_improper_angle_d 3.18
x_dihedral_angle_d 26.3
x_angle_deg 2.8
x_bond_d 0.03
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1532
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 235

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
AMoRE model building