X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 8.3% PEG 8000, 7.4% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.31 α = 90
b = 87.02 β = 90
c = 196.08 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2005-04-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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
2.8 50 92.5 0.151 -- -- 3.4 30838 28525 -- -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)
2.8 2.9 65.0 0.581 -- -- 2.6 --

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 2.8 42.37 -- -- 31422 23560 1188 78.76 -- 0.1959 0.19199 0.27577 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 2.8 2.868 -- 33 633 0.33 0.525 -- 29.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.499
Anisotropic B[1][1] -4.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.18
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.962
r_scbond_it 1.245
r_mcangle_it 2.281
r_mcbond_it 1.336
r_nbd_refined 0.302
r_gen_planes_refined 0.009
r_chiral_restr 0.079
r_dihedral_angle_4_deg 14.507
r_dihedral_angle_3_deg 16.702
r_dihedral_angle_2_deg 32.956
r_dihedral_angle_1_deg 5.283
r_angle_refined_deg 1.032
r_bond_refined_d 0.008
r_nbtor_refined 0.341
r_xyhbond_nbd_refined 0.278
r_symmetry_vdw_refined 0.31
r_symmetry_hbond_refined 0.258
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7082
Nucleic Acid Atoms 0
Heterogen Atoms 135
Solvent Atoms 115

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0005 refinement
HKL data processing