X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 290.0
Details PEG 4000, TRIS/HCl, ISOPROPANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.04 α = 90
b = 89.11 β = 90
c = 95.97 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-06-19
Diffraction Radiation
Monochromator Protocol
Diamond(111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3

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
1.85 26 99.8 0.058 -- -- 7.5 60245 60245 -- -- --
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)
1.85 1.95 99.2 0.201 -- 3.4 6.9 8705

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 1.85 26.0 -- 0.0 60237 57188 3049 99.78 0.1594 0.15947 0.15719 0.20227 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 1.85 1.873 2069 121 -- 0.167 0.251 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.71
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.1
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.37
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.198
r_nbd_refined 0.226
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.088
r_dihedral_angle_3_deg 19.134
r_dihedral_angle_1_deg 4.126
r_angle_other_deg 0.763
r_angle_refined_deg 1.423
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.162
r_xyhbond_nbd_other 0.032
r_symmetry_vdw_refined 0.262
r_symmetry_vdw_other 0.199
r_symmetry_hbond_refined 0.159
r_mcbond_it 1.107
r_mcangle_it 1.908
r_scbond_it 2.102
r_scangle_it 3.362
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5722
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 813

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection