X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Diffusion
pH 7.2
Temperature 298.0
Details CRYSTALS WERE GROWN BY BATCH METHOD BY MIXING 35 MICROLITERS OF A SOLUTION CONTAINING 25 MG/ML PROTEIN SOLUTION IN 0.02 M PHOSPHATE BUFFER AT PH 7.2, CONTAINING 0.15 M SODIUM CHLORIDE, 0.025 (W/V) SODIUM NITRITE, 20 TIMES MOLAR EXCESS OF METHYL-ALPHA-D-GALACTOSE WITH 23 MICROLITRES OF 30% PEG4000 SOLUTION IN THE SAME BUFFER. PEG4000, Sodium Phosphate, sodium chloride, sodium azide, LIQUID DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 182.11 α = 90
b = 182.11 β = 90
c = 44.99 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-11-20
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 28 98.9 0.11 -- -- 4.2 47085 11152 0.0 0.0 38.1
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)
3.0 3.1 98.2 0.44 -- -- -- 1115

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 3.0 20.0 0.0 0.0 11152 10646 868 95.9 -- 0.195 0.195 0.251 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 3.0 3.19 -- 133 1565 0.285 0.332 0.029 91.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 46.7
Anisotropic B[1][1] 5.6
Anisotropic B[1][2] 2.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.19
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.0
c_dihedral_angle_d 27.4
c_angle_deg 1.5
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.43
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3430
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 41

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