X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 278.0
Details 0.2M sodium citrate, 0.1M sodium cacodylate, 30% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.41 α = 90
b = 153.99 β = 90
c = 74.79 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-07-29
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9669 PETRA III, EMBL c/o DESY P13 (MX1)

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
2.4 102.94 100.0 0.163 -- -- 13.0 410396 31673 3.0 3.0 14.6
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)
2.4 2.51 100.0 0.626 -- 4.8 13.3 3806

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 2.4 102.94 -- 0.0 31666 30062 1593 99.97 -- 0.14052 0.13835 0.1822 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 2.4 2.462 -- 129 2199 0.19 0.225 -- 99.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.682
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.23
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.255
r_gen_planes_refined 0.011
r_bond_refined_d 0.018
r_mcangle_it 3.054
r_dihedral_angle_4_deg 17.813
r_scangle_other 5.138
r_dihedral_angle_1_deg 6.027
r_long_range_B_other 7.095
r_mcangle_other 3.054
r_bond_other_d 0.01
r_angle_other_deg 1.398
r_scbond_other 3.254
r_dihedral_angle_2_deg 46.526
r_mcbond_other 1.923
r_angle_refined_deg 1.792
r_dihedral_angle_3_deg 13.684
r_chiral_restr 0.105
r_gen_planes_other 0.008
r_long_range_B_refined 7.095
r_mcbond_it 1.924
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3532
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 547

Software

Software
Software Name Purpose
MxCuBE data collection
MOLREP phasing
REFMAC refinement version: 5.8.0049
XDS data reduction
Aimless data scaling version: 0.1.30