X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP: 18 DEGREES C SITTING DROP: 2 UL PROTEIN, 0.6 UL RESERVOIR

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.12 α = 90
b = 53.49 β = 110.91
c = 61.26 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 RIGAKU-MSC MIRRORS 2005-11-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MM007 -- -- --

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
2.1 100 100.0 0.13 -- -- 3.66 -- 16426 -- 2.0 --
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)
2.1 2.18 100.0 0.31 -- 2.8 3.6 --

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 2.1 57.26 -- -- -- 15595 831 99.95 -- 0.18681 0.18436 0.23286 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 2.1 2.155 -- 74 1132 0.179 0.273 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.306
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.58
Anisotropic B[2][2] -1.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.785
r_scbond_it 1.863
r_mcangle_it 1.258
r_mcbond_it 0.872
r_nbd_refined 0.218
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.088
r_dihedral_angle_4_deg 15.006
r_dihedral_angle_3_deg 13.485
r_dihedral_angle_2_deg 35.595
r_dihedral_angle_1_deg 5.953
r_angle_other_deg 0.819
r_angle_refined_deg 1.461
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_nbd_other 0.177
r_nbtor_refined 0.189
r_nbtor_other 0.081
r_xyhbond_nbd_refined 0.183
r_symmetry_vdw_refined 0.115
r_symmetry_vdw_other 0.246
r_symmetry_hbond_refined 0.237
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2109
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 205

Software

Computing
Computing Package Purpose
CRYSTAL CLEAR Data Reduction (intensity integration)
CRYSTAL CLEAR Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
AMORE model building