X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details sodium cacodylate, magnesium chloride, PEG 2000 MME, barium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.56 α = 90
b = 136.56 β = 90
c = 69.52 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-01-25
Diffraction Radiation
Monochromator Protocol
1.1 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
2.4 50 -- -- -- -- -- -- 24847 -- -- --

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 2.4 20.0 -- 0.0 -- 23557 1246 98.7 0.193 -- 0.191 0.246 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 2.4 2.461 -- 89 1623 0.273 0.317 -- 96.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 66.965
Anisotropic B[1][1] -1.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.5
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.7
r_nbd_refined 0.223
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.097
r_dihedral_angle_4_deg 19.371
r_dihedral_angle_3_deg 18.08
r_dihedral_angle_2_deg 37.729
r_dihedral_angle_1_deg 8.219
r_angle_other_deg 0.883
r_angle_refined_deg 1.624
r_bond_other_d 0.002
r_bond_refined_d 0.017
r_nbd_other 0.186
r_nbtor_refined 0.186
r_nbtor_other 0.091
r_xyhbond_nbd_refined 0.231
r_xyhbond_nbd_other 0.29
r_symmetry_vdw_refined 0.224
r_symmetry_vdw_other 0.234
r_symmetry_hbond_refined 0.264
r_mcbond_it 0.854
r_mcbond_other 0.145
r_mcangle_it 1.093
r_scbond_it 1.758
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3820
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 138

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.700 data extraction
REFMAC5 version: 5.2.0005 refinement