X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 6
Temperature 293.0
Details 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.38 α = 90
b = 30.61 β = 105.45
c = 63.75 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 MAR CCD 165 mm -- 2008-02-20
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW14A 0.827 Photon Factory AR-NW14A

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
1.21 50 81.6 0.048 -- -- 3.5 -- 32287 -- -3.0 --
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)
1.21 1.25 18.6 0.493 -- -- 1.9 727

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 1.21 17.02 -- 0.0 -- 32274 1601 82.07 -- 0.155 0.152 0.219 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 1.21 1.241 -- 20 484 0.266 0.289 -- 17.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.61
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.31
r_sphericity_bonded 6.441
r_symmetry_vdw_refined 0.21
r_sphericity_free 11.349
r_gen_planes_refined 0.014
r_scangle_it 7.227
r_mcangle_it 3.832
r_mcbond_it 2.673
r_dihedral_angle_1_deg 5.284
r_nbtor_refined 0.324
r_xyhbond_nbd_refined 0.166
r_symmetry_hbond_refined 0.153
r_angle_refined_deg 2.201
r_dihedral_angle_3_deg 14.058
r_rigid_bond_restr 3.6
r_chiral_restr 0.157
r_dihedral_angle_4_deg 16.278
r_scbond_it 5.279
r_dihedral_angle_2_deg 33.61
r_bond_refined_d 0.025
r_metal_ion_refined 0.492
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1217
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 146

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data reduction
HKL-2000 data scaling