X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details 17% 2-METHYL-2,4-PENTANEDIOL, 10% PEG 4000, 0.1M POTASSIUM CITRATE, PH 6.0, , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.05 α = 90
b = 121.05 β = 90
c = 260.76 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 0.9998 APS 17-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
3.3 19.78 97.5 0.01 0.01 -- 5.1 14555 14555 -- 1.0 87.0
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)
3.3 3.42 99.5 0.433 -- 3.2 5.3 1601

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 3.3 19.78 -- 0.0 13809 13809 738 97.47 0.20833 -- 0.20626 0.24901 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 3.3 3.383 1041 54 987 0.261 0.293 -- 99.14
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 90.8
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.899
r_scbond_it 0.811
r_angle_refined_deg 1.322
r_dihedral_angle_2_deg 36.899
r_dihedral_angle_4_deg 15.737
r_mcbond_it 0.428
r_mcangle_it 0.774
r_xyhbond_nbd_refined 0.148
r_gen_planes_refined 0.003
r_chiral_restr 0.085
r_bond_refined_d 0.01
r_nbd_refined 0.222
r_symmetry_vdw_refined 0.176
r_nbtor_refined 0.313
r_scangle_it 1.466
r_symmetry_hbond_refined 0.207
r_dihedral_angle_3_deg 20.152
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4015
Nucleic Acid Atoms 0
Heterogen Atoms 122
Solvent Atoms 20

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
PHASER phasing