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_sphericity_bonded 7.134
r_sphericity_free 16.795
r_rigid_bond_restr 5.198
r_nbd_refined 0.386
r_gen_planes_other 0.002
r_gen_planes_refined 0.009
r_chiral_restr 0.125
r_dihedral_angle_4_deg 20.84
r_dihedral_angle_3_deg 10.63
r_dihedral_angle_2_deg 39.459
r_dihedral_angle_1_deg 6.679
r_angle_other_deg 0.933
r_angle_refined_deg 1.742
r_bond_other_d 0.006
r_bond_refined_d 0.018
r_nbd_other 0.264
r_nbtor_other 0.094
r_xyhbond_nbd_refined 0.22
r_metal_ion_refined 0.143
r_symmetry_vdw_refined 0.032
r_symmetry_vdw_other 0.325
r_symmetry_hbond_refined 0.283
r_mcbond_it 3.455
r_mcbond_other 2.264
r_mcangle_it 4.354
r_scbond_it 5.464
r_scangle_it 6.747
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5.2 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2 refinement
EPMR model building
SCALA data reduction
MOSFLM data collection