X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.92 α = 90
b = 129.95 β = 95.81
c = 122.76 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-04-07
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 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
3.06 46.78 100.0 -- 0.133 -- 5.7 37836 37836 0.0 -2.0 75.0
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)
3.06 3.21 99.9 -- 0.849 1.1 -- 3738

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 3.061 46.78 -- 0.0 38314 37811 1900 98.78 0.236 0.236 0.243 0.292 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 3.061 3.141 2363 -- 2363 0.397 -- -- 83.68
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 99.74
Anisotropic B[1][1] -0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.36
Anisotropic B[2][2] 5.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.416
r_nbd_refined 0.186
r_gen_planes_other 0.001
r_gen_planes_refined 0.002
r_chiral_restr 0.053
r_dihedral_angle_4_deg 15.389
r_dihedral_angle_3_deg 14.653
r_dihedral_angle_2_deg 32.926
r_dihedral_angle_1_deg 5.544
r_angle_other_deg 0.681
r_angle_refined_deg 0.917
r_bond_other_d 0.001
r_bond_refined_d 0.006
r_nbd_other 0.155
r_nbtor_refined 0.172
r_nbtor_other 0.078
r_xyhbond_nbd_refined 0.132
r_metal_ion_refined 0.071
r_symmetry_vdw_refined 0.106
r_symmetry_vdw_other 0.126
r_symmetry_hbond_refined 0.174
r_mcbond_it 0.71
r_mcbond_other 0.035
r_mcangle_it 0.817
r_scbond_it 0.975
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10839
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 5

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.700 data extraction
REFMAC5 version: 5.2.0005 refinement