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_dihedral_angle_d 25.6
c_angle_deg 1.5
c_bond_d 0.007
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 124
Solvent Atoms 15

Software

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