X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.3
Temperature 291.0
Details 50mM resorcinol, 400mM NaCl, 1.0mg/ml protamine 30mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.52 α = 90
b = 61.84 β = 90
c = 86 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
CCD MAR CCD 165 mm -- 2005-06-23
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.918 SLS X06SA

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
2.24 30 98.6 0.107 -- -- 6.5 16106 15881 -- -- 33.7
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)
2.24 2.4 97.6 0.286 -- 4.1 2.8 2781

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 2.24 29.1 -- -- -- 15087 793 98.64 -- 0.20276 0.19929 0.26838 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 2.24 2.296 -- 53 1063 0.194 0.305 -- 96.29
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 26.301
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.831
r_chiral_restr 0.154
r_xyhbond_nbd_refined 0.345
r_dihedral_angle_3_deg 17.0
r_symmetry_hbond_refined 0.231
r_gen_planes_refined 0.009
r_mcangle_it 2.348
r_metal_ion_refined 0.205
r_symmetry_vdw_refined 0.221
r_dihedral_angle_4_deg 14.14
r_dihedral_angle_1_deg 7.492
r_scangle_it 5.135
r_scbond_it 3.407
r_nbtor_refined 0.312
r_mcbond_it 1.548
r_angle_refined_deg 1.941
r_nbd_refined 0.225
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2349
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 110

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
XDS data reduction
XSCALE data scaling
MOLREP phasing