X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 0.15M Sodium acetate, 20% PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.16 α = 90
b = 44.16 β = 90
c = 329.37 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Diamond (111), Ge(220) 2005-02-26
Diffraction Radiation
Monochromator Protocol
Toroidal mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.93930 ESRF ID14-4

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
1.2 17.34 96.1 -- 0.054 -- 4.6 59415 59415 0.0 0.0 14.6
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)
1.2 1.22 75.4 -- 0.3 2.4 1.9 2263

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 1.2 17.34 0.0 0.0 56307 56307 3010 96.13 0.1772 0.1772 0.1759 0.2015 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 1.199 1.23 3405 189 3216 0.215 0.251 -- 76.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.026
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.138
r_sphericity_bonded 8.187
r_scangle_it 6.235
r_rigid_bond_restr 2.994
r_nbd_refined 0.188
r_mcbond_it 3.489
r_scbond_it 5.071
r_nbtor_refined 0.302
r_chiral_restr 0.071
r_mcangle_it 4.527
r_xyhbond_nbd_refined 0.117
r_bond_refined_d 0.007
r_gen_planes_refined 0.004
r_dihedral_angle_4_deg 12.192
r_dihedral_angle_3_deg 11.242
r_metal_ion_refined 0.089
r_dihedral_angle_2_deg 35.868
r_sphericity_free 10.271
r_dihedral_angle_1_deg 5.53
r_symmetry_vdw_refined 0.144
r_angle_refined_deg 1.077
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1498
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 188

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing version: - CCP4