1VPA | pdb_00001vpa

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VGZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	277	0.2M Ca(OAc)2, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.23	α = 90
b = 144.23	β = 90
c = 53.724	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	APS	sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.67	49.35	98.28	0.109	11.46	4.51		18105			53.97

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.77	98.23		0.523	1.97	3.66	1772

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1vgz	2.67	49.35	16781	1313	98.26	0.20234	0.19879	0.21	0.24783	0.26	RANDOM	32.048

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]
1.9	0.95		1.9		-2.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.267
r_dihedral_angle_3_deg	16.021
r_dihedral_angle_4_deg	13.369
r_dihedral_angle_1_deg	6.071
r_scangle_it	1.617
r_angle_refined_deg	1.405
r_scbond_it	0.984
r_angle_other_deg	0.778
r_mcangle_it	0.672
r_mcbond_it	0.411
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.207
r_nbtor_refined	0.182
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_other	0.151
r_symmetry_hbond_refined	0.127
r_nbtor_other	0.085
r_mcbond_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	68

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement