X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details 25% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.52 α = 90
b = 119.12 β = 107.66
c = 60.89 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2014-07-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

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
1.55 100 94.7 0.061 -- 26.809 7.4 -- 84925 -- -- --
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)
1.55 1.58 61.9 0.362 -- -- 5.6 2786

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 1.55 59.56 -- 0.0 -- 80611 4297 94.19 -- 0.1852 0.1835 0.2181 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 1.546 1.586 -- 210 3721 0.35 0.368 -- 59.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.464
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_mcangle_it 3.1
r_angle_refined_deg 1.532
r_dihedral_angle_4_deg 15.681
r_dihedral_angle_1_deg 6.628
r_dihedral_angle_2_deg 34.893
r_mcbond_other 2.186
r_chiral_restr 0.088
r_mcbond_it 2.187
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 12.817
r_angle_other_deg 0.946
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4809
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 573

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
MOLREP phasing