X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 291.0
Details 20% (w/v) PEG 8000, 0.2 M NaCl and 0.1 M phosphate-citrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 234.49 α = 90
b = 234.49 β = 90
c = 57.32 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-11-07
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1

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
3.1 76.75 97.7 0.13 0.13 -- 4.0 62529 62529 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)
3.1 3.18 98.6 0.432 0.432 3.5 3.9 9259

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 3.1 76.75 0.0 0.0 62529 62516 3169 97.67 0.181 0.181 0.178 0.234 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 3.1 3.181 -- 214 4483 0.233 0.296 -- 97.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.197
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.267
r_scbond_it 2.404
r_mcangle_it 1.715
r_mcbond_it 0.864
r_gen_planes_refined 0.008
r_chiral_restr 0.132
r_dihedral_angle_4_deg 21.325
r_dihedral_angle_3_deg 19.993
r_dihedral_angle_2_deg 36.623
r_dihedral_angle_1_deg 7.116
r_angle_refined_deg 1.936
r_bond_refined_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14882
Nucleic Acid Atoms 0
Heterogen Atoms 256
Solvent Atoms 132

Software

Computing
Computing Package Purpose
Blue-Ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.9 data processing