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 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.89 α = 90
b = 63.56 β = 90
c = 69.1 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 -- 2003-10-17
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
1.14 46.63 99.64 0.04 0.04 -- 3.2 88464 88464 -- -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)
1.14 1.2 -- 0.284 0.284 1.5 1.3 6920

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 1.14 46.63 -- 0.0 88464 88464 4449 99.64 0.117 0.117 0.116 0.138 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 1.14 1.17 -- 152 2669 0.356 0.386 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 12.663
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.15
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.875
r_sphericity_free 16.976
r_rigid_bond_restr 3.471
r_nbd_refined 0.377
r_gen_planes_other 0.005
r_gen_planes_refined 0.01
r_chiral_restr 0.137
r_dihedral_angle_4_deg 11.996
r_dihedral_angle_3_deg 10.309
r_dihedral_angle_2_deg 41.098
r_dihedral_angle_1_deg 6.677
r_angle_other_deg 1.904
r_angle_refined_deg 1.869
r_bond_other_d 0.007
r_bond_refined_d 0.017
r_nbd_other 0.27
r_nbtor_other 0.102
r_xyhbond_nbd_refined 0.181
r_metal_ion_refined 0.121
r_symmetry_vdw_refined 0.193
r_symmetry_vdw_other 0.356
r_symmetry_hbond_refined 0.229
r_mcbond_it 3.083
r_mcbond_other 2.198
r_mcangle_it 3.977
r_scbond_it 5.283
r_scangle_it 6.73
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1654
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 371

Software

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