X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details Sodium Formate 0.5M-4M, Tris Base 100mM, pH 6.8-8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.07 α = 90
b = 121.88 β = 95.38
c = 170.1 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 315 -- 2008-02-21
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97995 ESRF ID23-1

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
1.92 55 99.5 0.086 0.086 -- 4.1 -- 123164 -- 2.1 21.2
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)
1.92 2.02 96.6 0.48 0.48 2.1 3.7 17384

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 1.92 30.0 2.0 2.0 123129 121860 1237 99.48 -- 0.196 0.19584 0.2133 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 1.92 1.97 -- 95 8432 0.299 0.304 -- 94.14
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 5.549
Anisotropic B[1][1] -0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.22
Anisotropic B[2][2] 0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.149
r_dihedral_angle_3_deg 14.211
r_nbd_refined 0.184
r_symmetry_vdw_refined 0.21
r_dihedral_angle_4_deg 21.834
r_chiral_restr 0.076
r_xyhbond_nbd_refined 0.158
r_dihedral_angle_1_deg 5.538
r_bond_refined_d 0.011
r_mcangle_it 0.496
r_mcbond_it 0.339
r_scangle_it 2.047
r_angle_refined_deg 1.127
r_dihedral_angle_2_deg 36.252
r_gen_planes_refined 0.004
r_scbond_it 1.199
r_nbtor_refined 0.295
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7372
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1284

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
ADSC data collection version: Quantum
MOSFLM data reduction
SCALA data scaling
SHELXS phasing