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_scangle_it 5.797
r_scbond_it 3.593
r_mcangle_it 2.273
r_mcbond_it 1.484
r_symmetry_hbond_refined 0.148
r_symmetry_vdw_other 0.288
r_symmetry_vdw_refined 0.215
r_bond_refined_d 0.034
r_bond_other_d 0.002
r_angle_refined_deg 2.306
r_angle_other_deg 1.213
r_dihedral_angle_1_deg 6.136
r_chiral_restr 0.148
r_gen_planes_refined 0.012
r_gen_planes_other 0.002
r_nbd_refined 0.214
r_nbd_other 0.255
r_nbtor_other 0.091
r_xyhbond_nbd_refined 0.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1050
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 125

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
BEAST Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement