X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 0.1 M sodium acetate, 2.0 M Na/K phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.06 α = 90
b = 86.06 β = 90
c = 266.84 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 103
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2009-05-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2

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
2.7 89.09 99.0 0.074 -- -- 5.83 -- 32427 -- -- 93.0
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)
2.7 2.8 99.7 0.521 -- 2.0 6.01 3157

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 2.7 43.03 -- -- 32427 30462 1626 98.83 0.21759 0.21759 0.21438 0.28052 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 2.7 2.77 -- 122 2234 0.362 0.452 -- 99.75
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 85.74
Anisotropic B[1][1] 4.35
Anisotropic B[1][2] 2.17
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.52
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_scbond_it 1.884
r_dihedral_angle_1_deg 7.357
r_gen_planes_refined 0.007
r_dihedral_angle_2_deg 41.333
r_angle_refined_deg 1.865
r_mcbond_it 0.525
r_dihedral_angle_4_deg 22.748
r_chiral_restr 0.123
r_scangle_it 3.036
r_dihedral_angle_3_deg 22.546
r_mcangle_it 0.987
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.497
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6435
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 17

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.5.0109
d*TREK data reduction
d*TREK data scaling