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 = 34.54 α = 90
b = 30.85 β = 105.65
c = 63.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2007-05-26
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 83.5 0.039 -- -- 3.2 -- 33220 -- -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 40.4 0.494 -- -- 2.0 1604

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 1.22 20.06 -- 0.0 -- 33209 1671 85.65 -- 0.156 0.153 0.207 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 1.221 1.253 -- 77 1433 0.257 0.366 -- 53.15
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.2
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.04
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.173
r_scbond_it 4.877
r_symmetry_vdw_refined 0.138
r_rigid_bond_restr 3.34
r_bond_refined_d 0.027
r_mcbond_it 2.492
r_dihedral_angle_4_deg 16.414
r_mcangle_it 3.286
r_dihedral_angle_2_deg 34.656
r_dihedral_angle_3_deg 13.834
r_angle_refined_deg 2.179
r_dihedral_angle_1_deg 4.924
r_xyhbond_nbd_refined 0.112
r_sphericity_bonded 6.02
r_sphericity_free 10.897
r_metal_ion_refined 0.617
r_scangle_it 6.234
r_nbtor_refined 0.313
r_nbd_refined 0.306
r_symmetry_hbond_refined 0.137
r_gen_planes_refined 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1217
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 162

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