X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.04 α = 90
b = 46.5 β = 112.02
c = 64.26 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 283
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Osmic mirrors 2002-12-06
Diffraction Radiation
Monochromator Protocol
Osmic mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.5 17.3 98.5 -- 0.118 -- 2.3 11207 11207 0.0 0.0 41.3
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)
2.5 2.59 99.9 -- -- -- -- --

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 2.5 17.3 -- 0.0 10099 10099 1100 98.51 0.18792 0.18792 0.18027 0.25737 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 2.5 2.564 -- 68 773 0.22 0.325 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC/TLS-REFINEMENT
Mean Isotropic B 12.728
Anisotropic B[1][1] -1.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.05
Anisotropic B[2][2] -1.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.41
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_bond_other_d 0.002
r_angle_other_deg 0.769
r_scbond_it 0.938
r_gen_planes_other 0.002
r_symmetry_vdw_other 0.224
r_nbtor_other 0.082
r_mcbond_it 0.411
r_angle_refined_deg 1.119
r_symmetry_vdw_refined 0.13
r_nbd_refined 0.182
r_symmetry_hbond_refined 0.182
r_dihedral_angle_1_deg 6.064
r_nbd_other 0.206
r_mcangle_it 0.769
r_scangle_it 1.605
r_chiral_restr 0.068
r_xyhbond_nbd_refined 0.166
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2793
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 98

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing