X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 298.0
Details Crystals were grown by the hanging-drop method. The drops contained 5 microlitres of 15mg/ml protein, a 20-fold molar excess of methyl-alpha-d-galactose in phosphate buffer pH 7.2 and 2ml of 35%(w/v) PEG 4000. 1ml of 35%(w/v) PEG 4000 was used as the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 134.53 α = 90
b = 125.91 β = 95.89
c = 138.79 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1997-10-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
3.3 28 93.1 0.12 -- -- 2.1 32900 69174 -- 0.0 24.9
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)
3.3 3.42 93.6 0.42 -- -- -- 3300

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 3.3 20.0 -- 0.0 31958 31958 1596 92.4 -- 0.204 0.204 0.242 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 3.3 3.51 -- 244 4945 0.303 0.32 0.02 90.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 47.4
Anisotropic B[1][1] -2.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.18
Anisotropic B[2][2] 9.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.95
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.02
c_dihedral_angle_d 27.7
c_angle_deg 1.5
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.65
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13925
Nucleic Acid Atoms 0
Heterogen Atoms 288
Solvent Atoms 80

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.4 Structure Refinement
Software
Software Name Purpose
CNS version: 0.4 refinement
AMORE model building