X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details PEGMME5000, Sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.81 α = 90
b = 52.61 β = 90
c = 60.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH osmic multi-layer mirror --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS 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 40 97.0 0.054 0.048 -- 4.2 -- 9437 1.0 0.0 35.0
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)
2.0 2.05 97.0 0.335 0.282 2.1 3.7 655

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 2.0 39.53 -- 0.0 -- 8498 938 96.1 0.19976 0.1997 0.1923 0.26754 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 2.0 2.052 -- 71 599 0.255 0.44 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.569
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_gen_planes_refined 0.012
r_nbd_refined 0.214
r_nbtor_other 0.091
r_symmetry_vdw_other 0.288
r_scangle_it 5.797
r_bond_refined_d 0.034
r_angle_refined_deg 2.306
r_chiral_restr 0.148
r_dihedral_angle_1_deg 6.136
r_mcangle_it 2.273
r_nbd_other 0.255
r_angle_other_deg 1.213
r_mcbond_it 1.484
r_xyhbond_nbd_refined 0.179
r_gen_planes_other 0.002
r_scbond_it 3.593
r_symmetry_hbond_refined 0.148
r_symmetry_vdw_refined 0.215
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1090
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 125

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
CCP4 data scaling version: (SCALA)
BEAST phasing