X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.1 M MES pH 6.5 21% PEG5000MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.89 α = 90
b = 58.15 β = 111.12
c = 47.66 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 MARMOSAIC 225 mm CCD -- 2005-03-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.979 SLS X06SA

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
1.5 13 97.0 0.077 -- -- 3.9 -- 27707 -- -3.0 --
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)
1.5 1.6 93.4 0.517 -- 2.3 3.5 --

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 1.5 13.0 -- -- -- 26319 1386 100.0 -- 0.20835 0.20559 0.26057 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 1.5 1.538 -- 91 1730 0.286 0.408 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.149
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.07
Anisotropic B[2][2] 1.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.23
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.311
r_dihedral_angle_1_deg 5.061
r_dihedral_angle_2_deg 33.186
r_gen_planes_refined 0.007
r_mcangle_it 1.37
r_angle_refined_deg 1.525
r_scangle_it 3.6
r_scbond_it 2.528
r_chiral_restr 0.107
r_xyhbond_nbd_refined 0.203
r_dihedral_angle_3_deg 14.792
r_metal_ion_refined 0.274
r_symmetry_vdw_refined 0.211
r_nbd_refined 0.224
r_symmetry_hbond_refined 0.18
r_mcbond_it 1.019
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 19.927
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1440
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 181

Software

Software
Software Name Purpose
XSCALE data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
XDS data reduction