X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details PEG 4000, 200mM Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.4 α = 90
b = 58.4 β = 90
c = 391.81 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2008-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID

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
2.15 50 93.4 0.096 -- -- 10.6 -- 21604 -- -- --
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)
2.15 2.23 73.4 0.227 -- -- 5.0 1627

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
FOURIER SYNTHESIS 2.15 44.94 -- 0.0 -- 21411 1099 93.14 -- 0.191 0.188 0.257 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 2.15 2.206 -- 60 1092 0.201 0.307 -- 71.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.069
Anisotropic B[1][1] 1.84
Anisotropic B[1][2] 0.92
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.77
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.46
r_scbond_it 3.01
r_mcangle_it 1.707
r_mcbond_it 1.171
r_symmetry_hbond_refined 0.257
r_symmetry_vdw_refined 0.235
r_bond_refined_d 0.021
r_angle_refined_deg 1.784
r_dihedral_angle_1_deg 5.477
r_dihedral_angle_2_deg 39.474
r_dihedral_angle_3_deg 16.433
r_dihedral_angle_4_deg 19.826
r_chiral_restr 0.124
r_gen_planes_refined 0.008
r_nbd_refined 0.231
r_nbtor_refined 0.309
r_xyhbond_nbd_refined 0.2
r_metal_ion_refined 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2891
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 295

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 refinement
HKL data processing