X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 295.5
Details PEG3000, Sodium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.65 α = 90
b = 88.07 β = 92.48
c = 83.74 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2001-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- 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
2.15 33.06 98.0 -- 0.038 -- 1.87 -- 24657 0.0 -3.0 32.6
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)
2.15 2.23 97.0 0.15723 0.544 1.65 1.83 2403

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 2.15 33.06 -- -- 25144 22763 1090 90.5 0.22 0.22 0.22 0.246 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 2.15 2.25 2401 117 2284 0.397 0.397 0.037 77.1
X Ray Diffraction 2.25 2.37 2512 117 2395 0.356 0.354 0.033 80.1
X Ray Diffraction 2.37 2.51 2713 128 2585 0.323 0.32 0.028 86.8
X Ray Diffraction 2.51 2.71 2854 149 2705 0.309 0.306 0.025 90.3
X Ray Diffraction 2.71 2.98 2976 142 2834 0.264 0.264 0.022 95.2
X Ray Diffraction 2.98 3.41 3071 140 2931 0.238 0.241 0.02 97.4
X Ray Diffraction 3.41 4.3 3088 134 2954 0.188 0.192 0.017 98.2
X Ray Diffraction 4.3 33.06 3148 163 2985 0.173 0.173 0.014 98.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.36
Anisotropic B[1][1] -12.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.35
Anisotropic B[2][2] 10.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.42
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_deg 26.4
x_dihedral_angle_d 1.4
x_angle_deg 1.4
x_torsion_impr_deg 0.79
x_bond_d 0.008
x_improper_angle_d 26.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.49
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3112
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 171

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing