X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.76 α = 90
b = 81.72 β = 109.9
c = 58.31 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 bent conical Si-mirror (Rh coating) 2004-11-08
Diffraction Radiation
Monochromator Protocol
bent cylindrical Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9734 APS 14-BM-C

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
2.7 20 97.8 0.113 0.113 -- 3.5 13294 13294 0.0 0.0 17.36
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)
2.7 2.8 98.7 0.546 0.546 3.47 3.4 1332

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 2.7 19.73 0.0 0.0 13275 13275 691 97.74 -- 0.209 0.205 0.291 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 2.7 2.769 959 49 910 0.282 0.356 -- 98.26
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 17.364
Anisotropic B[1][1] -2.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.56
Anisotropic B[2][2] 4.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.372
r_scbond_it 3.598
r_mcangle_it 2.444
r_mcbond_it 1.665
r_symmetry_hbond_refined 0.243
r_bond_refined_d 0.018
r_angle_refined_deg 1.92
r_dihedral_angle_1_deg 6.179
r_dihedral_angle_2_deg 40.287
r_dihedral_angle_3_deg 20.918
r_dihedral_angle_4_deg 29.452
r_chiral_restr 0.212
r_gen_planes_refined 0.007
r_nbd_refined 0.268
r_nbtor_refined 0.322
r_xyhbond_nbd_refined 0.17
r_symmetry_vdw_refined 0.291
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3845
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 3

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0019 refinement
HKL data processing