X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details PEG 3350, KMES, glycine, pH 6.5, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118 α = 90
b = 118 β = 90
c = 39.12 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2010-09-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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 25.1 99.9 0.093 -- -- 6.89 28587 28587 3.0 3.0 --
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)
2.2 2.28 100.0 0.555 -- 4.2 7.05 2818

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 25.1 -- 0.0 28533 28533 1420 99.65 -- 0.2643 0.2639 0.2844 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 2.2 2.256 -- 114 1915 0.291 0.3 -- 98.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.0152
Anisotropic B[1][1] -3.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.45
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.783
r_scbond_it 0.439
r_mcangle_it 0.528
r_mcbond_it 0.292
r_gen_planes_refined 0.004
r_chiral_restr 0.042
r_dihedral_angle_4_deg 9.995
r_dihedral_angle_3_deg 9.161
r_dihedral_angle_2_deg 27.952
r_dihedral_angle_1_deg 2.415
r_angle_refined_deg 1.105
r_bond_refined_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3088
Nucleic Acid Atoms 0
Heterogen Atoms 158
Solvent Atoms 21

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0109 refinement
Phaser molecular replacement
D*trek version: 9.9.8.8L data reduction
D*trek data collection