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_angle_deg 1.5
c_bond_d 0.008
c_dihedral_angle_d 27.4
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

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