1QMH

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QMIPDB ENTRY 1QMI, CHAIN A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.
Crystal Properties
Matthews coefficientSolvent content
2.8457

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.8α = 90
b = 133.5β = 90
c = 51γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATEMARRESEARCH1998-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9BNSLSX9B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.12097.20.04311.33.250057-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1783.40.2683.62.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QMI, CHAIN A2.11048203228693.60.2070.2040.276RANDOM37.1
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor21.1
p_staggered_tor17.5
p_scangle_it4.6
p_planar_tor4.3
p_mcangle_it3.8
p_scbond_it3
p_mcbond_it2.6
p_multtor_nbd0.261
p_singtor_nbd0.196
p_chiral_restr0.185
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor21.1
p_staggered_tor17.5
p_scangle_it4.6
p_planar_tor4.3
p_mcangle_it3.8
p_scbond_it3
p_mcbond_it2.6
p_multtor_nbd0.261
p_singtor_nbd0.196
p_chiral_restr0.185
p_xyhbond_nbd0.171
p_planar_d0.056
p_angle_d0.046
p_plane_restr0.029
p_bond_d0.022
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4971
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing