X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 100mM HEPES, 10% isopropanol, 200mM sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.66 α = 90
b = 128.66 β = 90
c = 165.45 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2006-10-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0 PAL/PLS 4A

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
1.33 30 95.6 0.082 -- -- -- 305983 292520 -- -- --
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)
1.33 1.38 60.1 0.418 -- 1.5 -- --

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 1.5 24.46 -- 0.0 213855 213577 10753 99.87 -- 0.169 0.168 0.183 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 1.5 1.539 -- 821 14890 0.211 0.238 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.066
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 37.813
r_nbtor_refined 0.296
r_angle_refined_deg 0.812
r_dihedral_angle_4_deg 10.942
r_scangle_it 2.016
r_nbd_refined 0.185
r_scbond_it 2.058
r_chiral_restr 0.071
r_symmetry_vdw_refined 0.139
r_dihedral_angle_1_deg 3.869
r_dihedral_angle_3_deg 11.407
r_rigid_bond_restr 2.269
r_sphericity_bonded 1.243
r_mcangle_it 0.724
r_symmetry_hbond_refined 0.106
r_bond_refined_d 0.006
r_mcbond_it 0.432
r_sphericity_free 1.362
r_gen_planes_refined 0.003
r_xyhbond_nbd_refined 0.103
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8436
Nucleic Acid Atoms 0
Heterogen Atoms 81
Solvent Atoms 1001

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.004
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing