X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 293.0
Details PEG 6000, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.41 α = 90
b = 99.7 β = 91.42
c = 182.83 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 1998-04-01
Diffraction Radiation
Monochromator Protocol
Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.954 ESRF BM14

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
1.83 35 83.1 -- 0.054 -- 3.06 169544 169544 0.0 3.0 24.6
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)
1.83 1.88 68.5 -- 0.255 2.5 3.01 --

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 1.83 20.0 -- 0.0 168613 160130 8483 83.01 0.14821 0.14821 0.14628 0.18467 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 1.83 1.911 -- 837 16160 0.198 0.237 -- 69.31
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 11.791
Anisotropic B[1][1] 2.89
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.18
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.96
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.512
r_angle_refined_deg 1.156
r_dihedral_angle_1_deg 5.499
r_dihedral_angle_2_deg 34.021
r_dihedral_angle_4_deg 17.243
r_mcbond_it 1.646
r_mcangle_it 2.082
r_chiral_restr 0.08
r_bond_refined_d 0.01
r_nbd_refined 0.21
r_symmetry_vdw_refined 0.195
r_symmetry_hbond_refined 0.159
r_xyhbond_nbd_refined 0.14
r_nbtor_refined 0.312
r_scbond_it 2.699
r_gen_planes_refined 0.004
r_dihedral_angle_3_deg 14.446
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18394
Nucleic Acid Atoms 0
Heterogen Atoms 211
Solvent Atoms 1848

Software

Software
Software Name Purpose
XDS data scaling
CCP4 data reduction
AMoRE phasing
REFMAC refinement version: 5.2.0005
ProDC data collection
CCP4 data scaling