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 PEG 4000, magnesium chloride, Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.48 α = 90
b = 66.46 β = 90
c = 70.05 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 ADSC QUANTUM 4 mirrors 2003-04-21
Diffraction Radiation
Monochromator Protocol
DOUBLE SI CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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 48.2 87.6 0.041 0.041 -- 2.5 61959 28704 2.0 2.0 41.7
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)
1.7 1.79 48.8 0.375 0.375 1.8 1.4 3006

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 48.2 -- -- 61959 25769 1377 86.99 0.20239 0.20239 0.2007 0.23261 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 1.744 -- 50 890 0.278 0.339 -- 41.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 41.687
Anisotropic B[1][1] 0.76
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.96
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.201
r_bond_refined_d 0.025
r_dihedral_angle_3_deg 16.302
r_scbond_it 3.54
r_symmetry_vdw_refined 0.383
r_nbtor_other 0.099
r_dihedral_angle_2_deg 35.821
r_gen_planes_refined 0.01
r_nbd_other 0.214
r_angle_refined_deg 2.182
r_symmetry_hbond_refined 0.2
r_scangle_it 4.64
r_angle_other_deg 1.058
r_gen_planes_other 0.001
r_bond_other_d 0.005
r_nbtor_refined 0.195
r_nbd_refined 0.235
r_symmetry_vdw_other 0.265
r_mcbond_it 2.023
r_mcbond_other 0.432
r_dihedral_angle_4_deg 21.699
r_xyhbond_nbd_other 0.149
r_chiral_restr 0.148
r_mcangle_it 2.352
r_dihedral_angle_1_deg 8.539
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.143
Luzzati ESD (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2313
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 132

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0003
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing