1VM7 | pdb_00001vm7

Crystal structure of Ribokinase (TM0960) from Thermotoga maritima at 2.15 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	0.4M (NH4)2Tartrate, 0.4% PEG-3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.142	α = 90
b = 45.265	β = 93.3
c = 77.26	γ = 90

Symmetry
Space Group	C 1 2 1

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	ADSC		2004-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

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	60.4	92.3	0.07	10	3.2		39375			37.9

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	2.05	61.2		0.682	1.3	1.9	1884

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	1gqt	2.15	60.4	32122	1676	97.96	0.19189	0.18954	0.2	0.23539	0.24	RANDOM	31.282

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]
1.99		0.85	-1.2		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.216
r_dihedral_angle_4_deg	21.355
r_dihedral_angle_3_deg	14.158
r_dihedral_angle_1_deg	6.023
r_scangle_it	2.376
r_scbond_it	1.559
r_angle_refined_deg	1.477
r_angle_other_deg	0.862
r_mcangle_it	0.839
r_mcbond_it	0.55
r_symmetry_hbond_refined	0.254
r_nbd_refined	0.202
r_symmetry_vdw_other	0.186
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.178
r_nbd_other	0.177
r_symmetry_vdw_refined	0.16
r_mcbond_other	0.16
r_nbtor_other	0.087
r_chiral_restr	0.081
r_xyhbond_nbd_other	0.059
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4537
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling