X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 35% PEG8K, 0.2 M ammonium sulfate, pH 6.2, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.54 α = 90
b = 131.18 β = 97.61
c = 90.32 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 RIGAKU SATURN 92 MICROMAX CONFOCAL 2005-04-29
Diffraction Radiation
Monochromator Protocol
-- None
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.541 -- --

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
2.5 50 96.8 0.087 -- -- 3.6 -- 66645 -- -- --
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)
2.5 2.59 91.1 0.472 -- -- 3.2 6244

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 2.5 50.0 -- 0.0 -- 66542 3377 96.54 -- 0.2265 0.2239 0.277 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 2.502 -- -- 246 4284 0.297 0.359 -- 88.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.3625
Anisotropic B[1][1] -2.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.52
Anisotropic B[2][2] -1.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.51
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.179
r_dihedral_angle_4_deg 14.327
r_dihedral_angle_1_deg 5.612
r_bond_refined_d 0.007
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.125
r_mcangle_it 0.589
r_symmetry_hbond_refined 0.099
r_dihedral_angle_3_deg 14.724
r_mcbond_it 0.318
r_scangle_it 1.073
r_dihedral_angle_2_deg 36.086
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.222
r_scbond_it 0.623
r_angle_refined_deg 1.154
r_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12156
Nucleic Acid Atoms 0
Heterogen Atoms 144
Solvent Atoms 819

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing