1NB9 | pdb_00001nb9

Crystal Structure of Riboflavin Kinase

X-RAY DIFFRACTION

---

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 cadodalyte, Mg acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.957	α = 90
b = 56.957	β = 90
c = 82.501	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	2002-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.7	50	97.5	0.03	42.2	7.2		17163	1	-3	26.838

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	1.7	1.76	90.3		0.263	5.1	3.4	1557

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1NB0	1.7	49.39	17150	16284	866	97.64	0.18476	0.18362	0.1864	0.20573	0.2097	RANDOM	20.827

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]
0.29	0.15		0.29		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.097
r_scangle_it	4.104
r_scbond_it	2.536
r_mcangle_it	1.799
r_angle_refined_deg	1.725
r_mcbond_it	1.002
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1177
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	55

Software

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