X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 292.0
Details HANGING-DROP METHOD AT 292 K WITH 1 MICROLITER OF RESERVOIR AND PROTEIN SOLUTION EACH. TRIS-HCL PH 8.5. PROTEIN: 17 MG/ML AF_EXO, 0.53 MM DS-DNA, 9 MM MES-NAOH PH 6, 0.28 M NACL.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.79 α = 90
b = 60.82 β = 91.22
c = 72.35 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRRORS 2005-02-10
Diffraction Radiation
Monochromator Protocol
SI-111 CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 -- BESSY 14.2

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
1.7 30 100.0 0.07 -- -- 7.8 -- 64871 -- -3.0 29.5
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)
1.7 1.74 99.9 0.44 -- 2.3 5.4 --

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 1.7 29.6 -- -- -- 63550 1314 100.0 -- 0.198 0.198 0.23 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 1.7 1.74 -- 100 4639 0.378 0.466 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.56
Anisotropic B[1][1] -0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] -1.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.88
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.675
r_chiral_restr 0.095
r_bond_refined_d 0.012
r_scbond_it 1.741
r_dihedral_angle_3_deg 14.12
r_symmetry_vdw_refined 0.162
r_symmetry_hbond_refined 0.115
r_mcangle_it 1.043
r_xyhbond_nbd_refined 0.095
r_dihedral_angle_1_deg 5.958
r_angle_refined_deg 1.398
r_dihedral_angle_4_deg 17.144
r_nbd_refined 0.204
r_dihedral_angle_2_deg 35.469
r_scangle_it 2.673
r_gen_planes_refined 0.005
r_nbtor_refined 0.303
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4204
Nucleic Acid Atoms 404
Heterogen Atoms 0
Solvent Atoms 220

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing