X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.01 α = 90
b = 82.94 β = 109.25
c = 58.58 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) --
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97946 SSRL BL11-1

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
2.6 20 92.5 0.105 0.105 -- 6.2 14355 14355 0.0 0.0 67.702
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)
2.6 2.69 67.5 0.535 0.535 2.35 3.1 1044

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 2.6 15.0 0.0 0.0 14267 14267 694 91.71 -- 0.198 0.195 0.249 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 2.6 2.666 704 43 661 0.299 0.386 -- 61.81
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 34.666
Anisotropic B[1][1] -3.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.16
Anisotropic B[2][2] 7.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.49
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.843
r_scbond_it 1.833
r_mcangle_it 1.261
r_mcbond_other 0.136
r_mcbond_it 0.789
r_symmetry_hbond_refined 0.105
r_symmetry_vdw_other 0.288
r_symmetry_vdw_refined 0.227
r_xyhbond_nbd_refined 0.17
r_nbtor_other 0.096
r_nbtor_refined 0.189
r_nbd_other 0.201
r_bond_refined_d 0.016
r_bond_other_d 0.001
r_angle_refined_deg 1.559
r_angle_other_deg 0.971
r_dihedral_angle_1_deg 6.399
r_dihedral_angle_2_deg 39.17
r_dihedral_angle_3_deg 18.596
r_dihedral_angle_4_deg 23.125
r_chiral_restr 0.079
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_nbd_refined 0.233
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3985
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 41

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
Phaser 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