X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 277.0
Details 0.1M MIB buffer, 25% w/v PEG 1500, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.33 α = 90
b = 65.33 β = 90
c = 71.38 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-07-02
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.979494 DIAMOND I02

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
1.49 71.38 95.1 -- 0.034 -- 2.4 53279 53279 -- -- --
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)
1.49 1.57 97.0 0.246 0.246 3.0 2.4 7928

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 1.5 30.19 -- 0.0 53279 51880 2638 95.01 -- 0.1619 0.16 0.1989 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 1.5 1.539 -- 221 3713 0.221 0.272 -- 97.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.4158
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 6.359
r_scbond_it 6.844
r_mcangle_it 4.03
r_mcbond_it 2.885
r_xyhbond_nbd_refined 0.195
r_gen_planes_refined 0.014
r_chiral_restr 0.185
r_dihedral_angle_2_deg 37.21
r_dihedral_angle_1_deg 5.1
r_angle_refined_deg 2.889
r_bond_refined_d 0.028
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2435
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 254

Software

Computing
Computing Package Purpose
GDA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA 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
Phaser version: 2.2.1 molecular replacement
SCALA version: 3.3.16 data reduction
Mosflm data collection