X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.4
Temperature 293.0
Details 10% aqu. acetone solution saturated with sodium nitrate, 25mg/ml lysozyme, pH 8.4, batch, temperature 293.0K, pH 8.40

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.64 α = 90
b = 85.64 β = 90
c = 67.93 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 10
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2004-06-30
Diffraction Radiation
Monochromator Protocol
SI 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 -- EMBL/DESY, Hamburg X13

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
1.46 70 100.0 0.038 -- -- 23.0 -- 25570 -- 3.5 --
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)
1.46 1.47 100.0 0.884 -- 3.5 13.2 --

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 1.46 70.0 -- 0.0 26041 25016 528 98.1 -- 0.183 0.183 0.198 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 1.46 1.5 -- 26 1844 0.204 0.262 -- 99.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.21
Anisotropic B[1][1] -0.14
Anisotropic B[1][2] -0.07
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.21
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.527
r_angle_refined_deg 1.98
r_angle_other_deg 1.027
r_nbtor_refined 0.189
r_mcangle_it 1.727
r_symmetry_metal_ion_refined 0.211
r_scangle_it 4.01
r_nbtor_other 0.09
r_dihedral_angle_2_deg 34.347
r_gen_planes_refined 0.011
r_chiral_restr 0.133
r_dihedral_angle_3_deg 13.55
r_gen_planes_other 0.001
r_bond_other_d 0.002
r_dihedral_angle_4_deg 17.941
r_nbd_other 0.204
r_scbond_it 2.622
r_nbd_refined 0.249
r_symmetry_vdw_other 0.311
r_metal_ion_refined 0.169
r_symmetry_hbond_refined 0.344
r_xyhbond_nbd_refined 0.303
r_mcbond_other 0.389
r_dihedral_angle_1_deg 11.106
r_bond_refined_d 0.021
r_mcbond_it 1.419
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 165

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing