X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details 30-35% 2-propanol, 0.6-0.7 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 21.59 α = 90
b = 38.15 β = 90
c = 78.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Mirrors 2001-02-11
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9795 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
1.5 39.2 95.0 0.071 -- -- 5.8 -- 10456 0.0 0.0 14.21
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)
1.5 1.53 71.8 0.196 -- -- -- --

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
MAD 1.5 39.22 -- 0.0 10412 9913 499 94.87 0.1905 0.1905 0.18892 0.22211 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 1.539 556 19 556 0.181 0.271 -- 72.15
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 15.641
Anisotropic B[1][1] -0.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.2
r_nbd_refined 0.26
r_gen_planes_other 0.002
r_gen_planes_refined 0.01
r_chiral_restr 0.118
r_dihedral_angle_2_deg 21.576
r_dihedral_angle_1_deg 4.944
r_angle_other_deg 0.886
r_angle_refined_deg 2.099
r_bond_other_d 0.001
r_bond_refined_d 0.02
r_xyhbond_nbd_refined 0.241
r_xyhbond_nbd_other 0.239
r_symmetry_vdw_refined 0.065
r_symmetry_vdw_other 0.165
r_symmetry_hbond_refined 0.262
r_mcbond_it 1.289
r_mcangle_it 2.073
r_scbond_it 3.227
r_scangle_it 4.862
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 522
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 78

Software

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