X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.6
Temperature 295.0
Details 1.8 M ammonium sulfate, 0.1M sodium acetate pH 5.6, VAPOR DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.15 α = 90
b = 130.15 β = 90
c = 150.43 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 ADSC QUANTUM 315 Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry 2006-12-10
Diffraction Radiation
Monochromator Protocol
Cryo-Cooled Si(111) double crystal. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C

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 49.21 -- -- 0.057 -- 12.9 -- 25407 -- -- --
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)
3.0 3.076 73.13 -- 0.602 2.25 5.5 --

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
SAD 3.0 49.21 -- -- -- 24119 1287 95.83 -- 0.23511 0.23325 0.27131 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 3.0 3.078 -- 77 1331 0.308 0.287 -- 73.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 144.096
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.682
r_scbond_it 1.673
r_mcangle_it 1.014
r_mcbond_it 0.516
r_gen_planes_refined 0.006
r_chiral_restr 0.107
r_dihedral_angle_4_deg 22.962
r_dihedral_angle_3_deg 20.966
r_dihedral_angle_2_deg 38.57
r_dihedral_angle_1_deg 7.059
r_angle_refined_deg 1.84
r_bond_refined_d 0.016
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.55
Luzzati Sigma A (Observed) 0.66
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.55
Luzzati Sigma A (R-Free Set) 0.73
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4145
Nucleic Acid Atoms 855
Heterogen Atoms 22
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC refinement
SOLVE model building
HKL-2000 data collection