2FV7

Crystal structure of human ribokinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RKS	pdb entries 1RKS, 1VM7
experimental model	PDB	1VM7	pdb entries 1RKS, 1VM7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	40% PEG-550MME, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.53	α = 90
b = 72.978	β = 91.08
c = 90.958	γ = 90

Symmetry
Space Group	P 1 21 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 QUANTUM 210		2005-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	50	99.3	0.046	13.6	3		34881

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18		97.8	0.261		3

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1RKS, 1VM7	2.1	30	34605	1770	99.186	0.201	0.201	0.1979	0.2484	thin shells	23.979

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]
-0.083		-0.018	0.062		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.534
r_dihedral_angle_4_deg	16.233
r_dihedral_angle_3_deg	12.543
r_dihedral_angle_1_deg	4.528
r_scangle_it	2.561
r_scbond_it	1.537
r_angle_refined_deg	1.462
r_scangle_other	1.286
r_mcangle_it	0.926
r_angle_other_deg	0.914
r_mcbond_it	0.493
r_mcangle_other	0.424
r_scbond_other	0.325
r_symmetry_vdw_other	0.223
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.192
r_nbd_other	0.183
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.11
r_mcbond_other	0.104
r_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4524
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	70

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction