X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details MPD, calcium chloride, bis-tris buffer, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.17 α = 90
b = 78.17 β = 90
c = 101.68 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 MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R

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
2.5 31 98.8 0.037 0.037 -- 11.8 12728 150605 -- -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)
2.5 2.54 96.1 0.113 0.113 8.3 -- 611

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 2.5 31.0 -3.0 0.0 12884 12728 1231 98.8 -- -- 0.222 0.268 The same test set was used as in the refinement of the native monomer structure 1qd5, which had been selected randomly.
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Anisotropic B[1][1] -8.882
Anisotropic B[1][2] -9.735
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.882
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.765
RMS Deviations
Key Refinement Restraint Deviation
c_angle_d 1.1358
c_bond_d 0.006075
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 90
Solvent Atoms 48

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CCP4 data scaling version: (TRUNCATE)