3VYA | pdb_00003vya

W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.05	293	100mM HEPES, 85%(v/v) 2-Methyl-2,4-pentanediol, 50%(w/v) polyethylene glycol 400, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.119	α = 90
b = 44.119	β = 90
c = 178.59	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315r		2012-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

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	2.4	20	99.8	0.128		15.3		4587

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	2.4	2.53	100		0.258		15

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	PDB ENTRY 1FLM	2.4	20	4323	209	99.91	0.20811	0.20499	0.2045	0.27348	0.2708	RANDOM	23.796

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]
0.41	0.2		0.41		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.27
r_dihedral_angle_4_deg	18.969
r_dihedral_angle_3_deg	15.528
r_dihedral_angle_1_deg	5.674
r_scangle_it	2.408
r_scbond_it	1.378
r_angle_refined_deg	1.116
r_mcangle_it	1.08
r_mcbond_it	0.575
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	908
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	31

Software

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