X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details MPD, calcium chloride, Bis-Tris buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.48 α = 90
b = 78.48 β = 90
c = 101.67 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2000 mirrors 1999-01-15
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS + NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 -- -- --

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 20 99.3 0.064 0.064 -- 10.0 -- 9276 -- -3.0 --
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 2.85 99.6 0.343 0.343 4.9 -- 453

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 20.0 0.0 0.0 9276 9231 900 99.2 -- -- 0.211 0.275 SAME AS SET USED IN REFINEMENT OF THE NATIVE STRUCTURE (1QD5). FROM THE ADDITIONAL REFLECTIONS 10% WAS RANDOMLY SELECTED FOR THE TEST SET
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Anisotropic B[1][1] -7.449
Anisotropic B[1][2] -12.686
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.449
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.899
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_angle_deg 1.5
c_dihedral_angle_d 25.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2091
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 39

Software

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