1P4M

CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NB0	PDB ENTRY 1NB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	NA CACODALYTE, MG ACETATE, PEG 8000 , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.097	α = 90
b = 57.097	β = 90
c = 82.482	γ = 120

Symmetry
Space Group	P 31 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	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC MIRROR	2002-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	1.8	30	99.3	0.053	21.4	4		14856		-3	28.35

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	1.8	1.86	95.2		0.854	1.2	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NB0	1.8	28.55	13300	719	94	0.188	0.186	0.227	RANDOM	22.07

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]
0.66	0.33		0.66		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.754
r_scangle_it	4.066
r_scbond_it	2.552
r_mcangle_it	1.823
r_angle_refined_deg	1.666
r_mcbond_it	1.017
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.206
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1177
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	59

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction