X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3
Temperature 293.0
Details 16% PEG3350, 0.1M SODIUM ACETATE, 14% TACSIMATE, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.55 α = 90
b = 51.55 β = 90
c = 50.87 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-11-22
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-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
1.71 50 99.8 0.7 -- -- 7.4 -- 13734 0.0 -5.0 --
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)
1.71 1.74 100.0 0.603 -- 2.9 7.3 --

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 1.71 22.99 -- -- -- 13734 729 99.85 0.17257 0.17257 0.17 0.22528 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 1.71 1.755 -- 61 991 0.213 0.264 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 20.753
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.378
r_scbond_it 2.149
r_mcangle_it 1.416
r_mcbond_it 0.861
r_symmetry_hbond_refined 0.094
r_bond_refined_d 0.014
r_angle_refined_deg 1.313
r_dihedral_angle_1_deg 5.424
r_dihedral_angle_2_deg 30.879
r_dihedral_angle_3_deg 14.042
r_dihedral_angle_4_deg 17.986
r_chiral_restr 0.09
r_gen_planes_refined 0.006
r_nbd_refined 0.202
r_nbtor_refined 0.312
r_xyhbond_nbd_refined 0.155
r_symmetry_vdw_refined 0.196
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 984
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 93

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.3.0037 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.3.0037 refinement
PHASER model building
HKL-3000 data collection