X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.2 M sodium chloride, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.44 α = 90
b = 120.44 β = 90
c = 98 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 Kohzu HLD-4 Double Crystal 2009-11-20
Diffraction Radiation
Monochromator Protocol
Diamond 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID -- APS 31-ID

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
2.1 20 99.9 -- 0.132 -- 13.9 40392 40352 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)
2.1 2.21 100.0 -- 0.612 4.9 13.4 --

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 2.1 19.8 -- -- 40392 40352 2176 99.83 0.1671 0.1671 0.16538 0.19883 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 2.1 2.154 -- 152 2679 0.188 0.224 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.175
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.09
r_dihedral_angle_2_deg 34.603
r_dihedral_angle_4_deg 15.336
r_gen_planes_other 0.003
r_bond_refined_d 0.028
r_dihedral_angle_3_deg 15.521
r_dihedral_angle_1_deg 6.633
r_chiral_restr 0.139
r_angle_other_deg 1.028
r_gen_planes_refined 0.011
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3152
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 279

Software

Software
Software Name Purpose
SPEC data collection
PHASER phasing
REFMAC refinement version: 5.6.0111
MOSFLM data reduction
SCALA data scaling