1MEO

human glycinamide ribonucleotide Transformylase at pH 4.2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MEJPDB ENTRY 1MEJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22821.9-2.1M Ammonium Sulfate, 100mM Na Acetate pH 4.2-4.6, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
4.572.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.13α = 90
b = 78.13β = 90
c = 230.91γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 92001-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.976SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7243.9294.80.07223.42.440379-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.721.78990.4181.651.916675

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MEJ1.7243.85450304037944580.2260.2260.2230.24RANDOM18.691
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.590.290.59-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.217
r_dihedral_angle_1_deg3.641
r_scangle_it3.352
r_scbond_it1.902
r_angle_refined_deg1.142
r_mcangle_it1.135
r_mcbond_it0.57
r_symmetry_hbond_refined0.499
r_nbd_refined0.219
r_symmetry_vdw_refined0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.217
r_dihedral_angle_1_deg3.641
r_scangle_it3.352
r_scbond_it1.902
r_angle_refined_deg1.142
r_mcangle_it1.135
r_mcbond_it0.57
r_symmetry_hbond_refined0.499
r_nbd_refined0.219
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.11
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1531
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms10

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction