X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 0.1M MIB buffer, 25% PEG1500, 1mM TCEP, 1mM ATP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.71 α = 90
b = 84.07 β = 90
c = 151.13 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 -- 2009-05-06
Diffraction Radiation
Monochromator Protocol
Horizontal focusing Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.917 CHESS A1

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
2.69 50 96.2 0.076 -- -- 11.7 21478 20662 0.0 0.0 --
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)
2.69 2.8 91.2 0.639 -- -- 10.7 1944

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 2.69 20.0 -- 0.0 21478 20610 1058 95.78 0.2128 0.2128 0.2104 0.2568 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 2.69 2.757 -- 66 1125 0.325 0.38 -- 84.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.4792
Anisotropic B[1][1] -1.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.5
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_chiral_restr 0.088
r_dihedral_angle_4_deg 15.421
r_dihedral_angle_3_deg 17.143
r_dihedral_angle_2_deg 37.427
r_dihedral_angle_1_deg 5.995
r_angle_refined_deg 1.359
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4370
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 52

Software

Computing
Computing Package Purpose
ADX package Data Collection
HKL-2000 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: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction