X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details well solution: 11%(w/v) PEG3350, 0.1 M MES; protein solution: 50 mM NaCl, 5 mM Tris, 0.5 mM EDTA, 20 mM benzamidine-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.42 α = 90
b = 70.41 β = 90
c = 121.41 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate mirrors 2007-11-01
Diffraction Radiation
Monochromator Protocol
Si [111], horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8148 EMBL/DESY, Hamburg X11

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
2.55 45.98 97.9 0.095 -- -- 5.9 -- 19349 -- -3.0 30.892
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)
2.55 2.6 97.4 0.472 -- 4.3 5.8 1066

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 2.55 45.98 -- 0.0 -- 19342 989 97.92 0.231 0.231 0.229 0.278 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 2.55 2.616 1438 78 1318 0.337 0.428 -- 97.08
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 48.887
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.71
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 0.429
r_xyhbond_nbd_refined 0.115
r_dihedral_angle_4_deg 16.582
r_chiral_restr 0.071
r_mcangle_it 1.046
r_angle_other_deg 0.824
r_dihedral_angle_3_deg 13.929
r_nbd_other 0.188
r_angle_refined_deg 1.163
r_mcbond_other 0.096
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 8.419
r_symmetry_vdw_other 0.157
r_symmetry_vdw_refined 0.097
r_dihedral_angle_2_deg 36.278
r_nbtor_refined 0.173
r_nbtor_other 0.081
r_nbd_refined 0.19
r_mcbond_it 0.623
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.082
r_bond_other_d 0.002
r_scangle_it 0.674
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3065
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 90

Software

Software
Software Name Purpose
XSCALE data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.006
MAR345dtb data collection
XDS data reduction