X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 295.0
Details 0.1M Tris-HCl, pH 6.7, 2.5M sodium formate, 10mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.12 α = 90
b = 37.05 β = 115.29
c = 64.85 γ = 90
Symmetry
Space Group P 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Mirrors 2010-10-29
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator (Cryogenically cooled) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A

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
2.48 50 81.3 0.094 -- -- 3.8 8601 8546 2.0 2.0 --
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)
2.478 2.542 99.0 0.575 -- -- 3.6 --

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 2.478 31.92 -- -- -- 6667 336 80.9 -- 0.18596 0.18314 0.24786 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 2.478 2.542 -- 18 214 0.228 0.313 -- 38.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.087
Anisotropic B[1][1] -24.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.36
Anisotropic B[2][2] -9.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 34.83
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.007
r_gen_planes_refined 0.008
r_chiral_restr 0.133
r_dihedral_angle_4_deg 18.191
r_dihedral_angle_3_deg 22.732
r_dihedral_angle_2_deg 38.065
r_dihedral_angle_1_deg 7.227
r_angle_other_deg 3.844
r_angle_refined_deg 2.39
r_bond_other_d 0.003
r_bond_refined_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1506
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 42

Software

Computing
Computing Package Purpose
CBASS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement
SCALEPACK data reduction
DENZO data collection