X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.39 α = 90
b = 63.59 β = 90
c = 68.85 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-05-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.00000 ALS 8.3.1

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
1.28 46.63 96.27 0.075 0.075 -- 3.1 59870 59870 -3.0 -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)
1.28 1.35 -- 0.475 0.475 1.7 2.2 --

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 1.28 46.63 -- 0.0 59869 59869 3027 96.27 0.125 0.125 0.124 0.158 inherited from PDB entry 2AGE
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 1.28 1.313 -- 124 2211 0.264 0.369 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 8.963
Anisotropic B[1][1] 0.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 5.198
r_angle_other_deg 0.933
r_xyhbond_nbd_refined 0.22
r_dihedral_angle_2_deg 39.459
r_scbond_it 5.464
r_dihedral_angle_1_deg 6.679
r_symmetry_vdw_other 0.325
r_sphericity_free 16.795
r_mcbond_other 2.264
r_bond_other_d 0.006
r_dihedral_angle_4_deg 20.84
r_symmetry_hbond_refined 0.283
r_bond_refined_d 0.018
r_scangle_it 6.747
r_nbtor_other 0.094
r_symmetry_vdw_refined 0.032
r_nbd_refined 0.386
r_mcbond_it 3.455
r_gen_planes_other 0.002
r_nbd_other 0.264
r_mcangle_it 4.354
r_chiral_restr 0.125
r_metal_ion_refined 0.143
r_angle_refined_deg 1.742
r_gen_planes_refined 0.009
r_dihedral_angle_3_deg 10.63
r_sphericity_bonded 7.134
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1648
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 357

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
EPMR phasing
REFMAC refinement version: 5.2
CCP4 data scaling version: (SCALA)