X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details ammonium sulfate, bis-tris propane, calcium chloride, 4-nitrophenyl 4-guanidinobenzoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.45 α = 90
b = 57.91 β = 90
c = 66.77 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 -- 2005-04-01
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
1.13 43.85 99.97 0.056 0.056 -- 3.5 75171 75171 -- -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)
1.13 1.19 -- 0.533 0.533 1.5 1.6 --

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 1.13 43.85 -- 0.0 75169 75169 3830 99.97 0.12 0.12 0.119 0.146 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 1.13 1.159 -- 186 3475 0.322 0.326 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 8.644
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.128
r_symmetry_hbond_refined 0.271
r_symmetry_vdw_refined 0.279
r_xyhbond_nbd_refined 0.211
r_mcbond_it 2.719
r_dihedral_angle_3_deg 11.903
r_sphericity_bonded 5.3
r_angle_refined_deg 1.794
r_gen_planes_other 0.011
r_scangle_it 5.931
r_angle_other_deg 2.686
r_nbd_refined 0.364
r_dihedral_angle_4_deg 18.001
r_bond_refined_d 0.016
r_mcangle_it 3.563
r_symmetry_vdw_other 0.282
r_rigid_bond_restr 5.558
r_nbd_other 0.26
r_bond_other_d 0.004
r_chiral_restr 0.148
r_mcbond_other 1.429
r_dihedral_angle_2_deg 40.355
r_scbond_it 4.63
r_gen_planes_refined 0.01
r_nbtor_other 0.093
r_sphericity_free 13.627
r_dihedral_angle_1_deg 6.609
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1674
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 359

Software

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