X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.9
Temperature 291.0
Details PEG 3350, sodium acetate, glucose, cymal-2, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.57 α = 90
b = 56.57 β = 90
c = 390.05 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-02-02
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.127 ALS 8.3.1

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
2.8 24.47 93.0 0.069 0.069 -- -- 10076 9368 0.0 3.0 59.8
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)
2.8 2.98 81.5 -- -- -- -- --

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 2.8 24.47 3.0 0.0 10075 9368 500 93.0 0.228 0.228 0.216 0.264 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 2.8 2.93 917 45 -- 0.281 0.369 0.055 76.7
X Ray Diffraction 2.93 3.08 1141 62 -- 0.291 0.38 0.048 93.8
X Ray Diffraction 3.08 3.27 1174 65 -- 0.262 0.352 0.044 95.4
X Ray Diffraction 3.27 3.53 1179 70 -- 0.234 0.295 0.035 95.5
X Ray Diffraction 3.53 3.88 1163 48 -- 0.224 0.279 0.04 95.5
X Ray Diffraction 3.88 4.44 1200 63 -- 0.194 0.271 0.034 94.4
X Ray Diffraction 4.44 5.58 1248 64 -- 0.195 0.215 0.027 96.5
X Ray Diffraction 5.58 24.47 1346 83 -- 0.232 0.228 0.025 94.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 60.08
Anisotropic B[1][1] 8.9
Anisotropic B[1][2] 14.57
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.81
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.7
c_improper_angle_d 1.31
x_angle_deg 1.6
x_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.48
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1892
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 40

Software

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