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_scangle_it 1.073
r_scbond_it 0.623
r_mcangle_it 0.589
r_mcbond_it 0.318
r_symmetry_hbond_refined 0.099
r_bond_refined_d 0.007
r_angle_refined_deg 1.154
r_dihedral_angle_1_deg 5.612
r_dihedral_angle_2_deg 36.086
r_dihedral_angle_3_deg 14.724
r_dihedral_angle_4_deg 14.327
r_chiral_restr 0.069
r_gen_planes_refined 0.003
r_nbd_refined 0.179
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.125
r_symmetry_vdw_refined 0.222
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

Computing
Computing Package Purpose
HKL2000 Data Reduction (intensity integration)
HKL2000 Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0019 refinement
CNS molecular replacement
HKL data reduction
DENZO data collection