X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 20% PEG3350, 200mM calcium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.35 α = 90
b = 76.14 β = 90
c = 81.79 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2009-11-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 PHOTON FACTORY AR-NW12A

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
2.2 55.73 99.9 -- 0.13 -- 7.2 22362 22345 -- -- 29.4
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)
2.2 2.24 99.8 -- 0.691 2.8 7.0 1100

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 2.2 55.73 -- -- 21179 21156 1140 99.89 -- 0.20173 0.19801 0.27282 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 2.199 2.256 1609 81 1528 0.22 0.292 -- 99.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.054
Anisotropic B[1][1] -0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.844
r_scbond_it 2.283
r_mcangle_it 1.507
r_mcbond_it 0.781
r_gen_planes_refined 0.006
r_chiral_restr 0.105
r_dihedral_angle_4_deg 19.439
r_dihedral_angle_3_deg 17.061
r_dihedral_angle_2_deg 38.521
r_dihedral_angle_1_deg 5.882
r_angle_refined_deg 1.374
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3171
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 261

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.5.0088 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0088 refinement
AMoRE model building
HKL-2000 data collection