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_sphericity_bonded 5.3
r_sphericity_free 13.627
r_rigid_bond_restr 5.558
r_nbd_refined 0.364
r_gen_planes_other 0.011
r_gen_planes_refined 0.01
r_chiral_restr 0.148
r_dihedral_angle_4_deg 18.001
r_dihedral_angle_3_deg 11.903
r_dihedral_angle_2_deg 40.355
r_dihedral_angle_1_deg 6.609
r_angle_other_deg 2.686
r_angle_refined_deg 1.794
r_bond_other_d 0.004
r_bond_refined_d 0.016
r_nbd_other 0.26
r_nbtor_other 0.093
r_xyhbond_nbd_refined 0.211
r_metal_ion_refined 0.128
r_symmetry_vdw_refined 0.279
r_symmetry_vdw_other 0.282
r_symmetry_hbond_refined 0.271
r_mcbond_it 2.719
r_mcbond_other 1.429
r_mcangle_it 3.563
r_scbond_it 4.63
r_scangle_it 5.931
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1621
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 359

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