X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.05 α = 90
b = 84.27 β = 108.48
c = 58.21 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 SBC mirrors --
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97934 APS 19-BM

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
2.35 50 95.7 0.097 0.097 -- 3.8 20938 20938 0.0 0.0 30.69
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)
2.35 2.43 93.6 0.415 0.415 1.8 3.2 2028

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 2.39 33.37 0.0 0.0 17913 17913 920 87.46 -- 0.241 0.238 0.296 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 2.39 2.45 1443 82 1361 0.215 0.37 -- 95.75
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 24.294
Anisotropic B[1][1] 0.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.03
Anisotropic B[2][2] 0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.39
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.613
r_scbond_it 1.134
r_mcangle_it 0.972
r_mcbond_other 0.101
r_mcbond_it 0.881
r_symmetry_hbond_refined 0.134
r_symmetry_vdw_other 0.289
r_symmetry_vdw_refined 0.462
r_xyhbond_nbd_refined 0.67
r_nbtor_other 0.088
r_nbtor_refined 0.171
r_nbd_other 0.194
r_bond_refined_d 0.01
r_bond_other_d 0.001
r_angle_refined_deg 1.341
r_angle_other_deg 1.025
r_dihedral_angle_1_deg 5.167
r_dihedral_angle_2_deg 37.83
r_dihedral_angle_3_deg 16.721
r_dihedral_angle_4_deg 18.369
r_chiral_restr 0.105
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_nbd_refined 0.206
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3982
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 216

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