X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details protein solution : 25mg/ml, 1M NaCl, 10mM Tris pH 7.9. well solution : 25% MPD, 20 mM CaCl2, 0.1 M acetate buffer pH 4.6 mix 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.14 α = 90
b = 163.77 β = 90
c = 60.16 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2005-02-07
Diffraction Radiation
Monochromator Protocol
SI 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.039 APS 22-BM

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
1.85 40 100.0 0.05 0.05 -- 6.0 22066 22066 -3.0 -3.0 31.6
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)
1.85 1.92 100.0 0.832 0.832 2.4 6.0 2165

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 1.85 30.0 -- -3.0 20912 20912 1130 100.0 0.19207 0.19207 0.18934 0.24731 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 1.85 1.898 -- 97 1512 0.257 0.314 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.318
Anisotropic B[1][1] -0.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.11
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.021
r_xyhbond_nbd_refined 0.212
r_scbond_it 6.772
r_symmetry_hbond_refined 0.227
r_chiral_restr 0.164
r_mcangle_it 5.602
r_scangle_it 10.112
r_gen_planes_refined 0.008
r_dihedral_angle_1_deg 7.109
r_symmetry_vdw_refined 0.244
r_mcbond_it 3.269
r_angle_refined_deg 1.934
r_nbd_refined 0.228
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1547
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 135

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing