X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 277.0
Details MOPS buffer, PEG MME 2k, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.59 α = 72.61
b = 63.97 β = 74.09
c = 64.02 γ = 73.68
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2020 mirrors --
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 1.5418 -- --

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
2.28 30 95.7 -- 0.068 -- 6.4 32764 31355 0.0 -3.0 24.2
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)
2.28 2.3 93.6 -- 0.163 3.9 -- --

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 2.28 29.88 -- 0.0 -- 29743 1612 100.0 -- 0.16873 0.16581 0.22278 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 2.28 -- -- -- -- 0.176 0.222 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.844
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] -0.27
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] -0.24
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.173
r_scbond_it 1.982
r_mcangle_it 1.122
r_nbd_refined 0.229
r_gen_planes_refined 0.005
r_chiral_restr 0.087
r_dihedral_angle_3_deg 16.063
r_dihedral_angle_1_deg 3.146
r_angle_refined_deg 1.329
r_bond_refined_d 0.011
r_xyhbond_nbd_refined 0.145
r_metal_ion_refined 0.112
r_symmetry_vdw_refined 0.238
r_symmetry_hbond_refined 0.204
r_mcbond_it 0.597
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.226
Luzzati Sigma A (Observed) 0.179
Luzzati ESD (R-Free Set) 0.241
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6067
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 416

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection