X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 298.0
Details 15% PEG 4000, 0.1 M HEPES, 40 mM beta-mercaptoethanol, 6% isopropanol, 3% ethanol , pH 7.8, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.98 α = 90
b = 43.24 β = 90
c = 158.23 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 RIGAKU RAXIS IV++ varimax optics 2006-07-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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 41.7 97.5 0.043 -- -- 3.4 20349 19840 -- -- 30.6
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)
2.0 2.07 93.3 0.174 -- 7.1 2.8 1976

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 2.0 41.7 -- -- -- 19800 1007 97.77 0.227 -- 0.225 0.267 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 2.0 2.052 -- 68 1285 0.265 0.398 -- 93.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.707
Anisotropic B[1][1] -0.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.964
r_dihedral_angle_2_deg 32.499
r_nbd_refined 0.171
r_angle_refined_deg 1.025
r_nbtor_refined 0.302
r_mcbond_it 0.718
r_scbond_it 0.892
r_chiral_restr 0.069
r_scangle_it 1.315
r_symmetry_hbond_refined 0.097
r_symmetry_vdw_refined 0.127
r_xyhbond_nbd_refined 0.104
r_dihedral_angle_3_deg 14.134
r_dihedral_angle_4_deg 18.571
r_bond_refined_d 0.007
r_gen_planes_refined 0.003
r_mcangle_it 1.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2244
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 206

Software

Software
Software Name Purpose
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 1.401
CrystalClear data collection
DENZO data reduction
AMoRE phasing