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 100mM Tris pH=8.5, and 3.5M NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.32 α = 90
b = 93.32 β = 90
c = 157.02 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2006-04-02
Diffraction Radiation
Monochromator Protocol
double crystal monochromator Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97912 APS 19-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
2.41 44.73 98.7 0.127 -- -- 7.2 32091 31670 0.0 0.0 --
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)
2.41 2.5 88.7 0.578 -- 2.78 4.0 2791

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
SAD 2.41 44.73 -- 0.0 27925 27925 3118 99.42 0.19315 0.19315 0.19049 0.21661 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 2.41 2.472 -- 216 1933 0.254 0.314 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.346
Anisotropic B[1][1] 2.95
Anisotropic B[1][2] 1.48
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.43
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.082
r_nbd_refined 0.218
r_dihedral_angle_2_deg 36.887
r_mcbond_it 0.852
r_xyhbond_nbd_refined 0.157
r_bond_refined_d 0.014
r_dihedral_angle_3_deg 19.196
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 22.018
r_mcangle_it 1.477
r_scangle_it 3.145
r_symmetry_hbond_refined 0.123
r_symmetry_vdw_refined 0.204
r_chiral_restr 0.113
r_dihedral_angle_1_deg 6.232
r_angle_refined_deg 1.498
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2867
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 225

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0000
HKL-2000 data reduction
HKL-2000 data scaling
HKL-3000 phasing
SHELXE model building
SOLVE phasing
RESOLVE phasing
ARP/wARP model building