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_angle_deg 1.5
c_bond_d 0.008
c_dihedral_angle_d 27.7
c_improper_angle_d 1.02
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

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.4
DENZO data reduction
SCALEPACK data scaling