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 9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.02 α = 90
b = 81.01 β = 114.56
c = 57.67 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 -- 2008-02-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2

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
1.95 50 96.4 0.065 0.65 -- 3.8 -- 36050 0.0 0.0 29.304
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)
1.95 2.02 90.9 0.376 0.376 4.4 3.8 3011

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 1.95 14.91 0.0 0.0 36050 31902 3295 99.5 0.194 0.194 0.193 0.226 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 1.95 2.0 -- 247 2370 0.241 0.273 -- 99.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.014
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_gen_planes_refined 0.004
r_mcangle_it 1.177
r_angle_refined_deg 1.171
r_dihedral_angle_3_deg 14.357
r_symmetry_vdw_refined 0.144
r_nbd_refined 0.188
r_scbond_it 1.546
r_dihedral_angle_2_deg 32.171
r_mcbond_it 0.699
r_bond_refined_d 0.009
r_scangle_it 2.313
r_dihedral_angle_1_deg 5.562
r_dihedral_angle_4_deg 18.696
r_symmetry_hbond_refined 0.131
r_xyhbond_nbd_refined 0.122
r_chiral_restr 0.084
r_nbtor_refined 0.293
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3198
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 175

Software

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