X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 10-20% PEG 20K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.78 α = 90
b = 79.15 β = 90
c = 139.22 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
CCD MAR CCD 165 mm SI[111] horizontally focussing monochromator 2006-05-19
Diffraction Radiation
Monochromator Protocol
SI[111] horizontally focussing monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8162 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
2.3 40 99.3 0.064 -- -- 10.8 25671 25480 -- -- 56.5
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)
2.3 2.38 97.5 0.599 -- 2.37 5.3 2442

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 2.3 40.0 -- -- 25805 24234 806 99.31 -- 0.19025 0.18811 0.25716 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 2.3 2.36 1854 69 1731 0.231 0.324 -- 97.19
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 72.418
Anisotropic B[1][1] -2.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.97
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 39.544
r_angle_refined_deg 1.86
r_dihedral_angle_3_deg 16.405
r_mcangle_it 1.141
r_dihedral_angle_1_deg 6.687
r_scbond_it 1.894
r_mcbond_it 0.81
r_xyhbond_nbd_refined 0.177
r_symmetry_vdw_refined 0.229
r_symmetry_hbond_refined 0.198
r_chiral_restr 0.101
r_scangle_it 2.743
r_dihedral_angle_4_deg 18.307
r_gen_planes_refined 0.006
r_nbtor_refined 0.314
r_bond_refined_d 0.021
r_nbd_refined 0.204
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3343
Nucleic Acid Atoms 0
Heterogen Atoms 350
Solvent Atoms 268

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing