1BU5 | pdb_00001bu5

X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FX2	WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.75	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.38	α = 90
b = 62.31	β = 127.26
c = 77.42	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	295	IMAGE PLATE	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.5		SRS	PX9.5

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	1.83	20	79.9	0.042	15.3	1.5		26539		-3	23

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	1.83	1.86	83.2		0.23	2.5	1.5

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2	1.83	10	26539	2037	81	0.169	0.167	0.202	RANDOM	27.1

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	25.46
p_staggered_tor	20.18
p_scangle_it	10.3
p_scbond_it	6.8
p_mcangle_it	4.4
p_mcbond_it	3.18
p_planar_tor	2.3
p_multtor_nbd	0.25
p_singtor_nbd	0.23
p_chiral_restr	0.17
p_angle_d	0.048
p_planar_d	0.048
p_bond_d	0.017
p_plane_restr	0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2208
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	64

Software

Software
Software Name	Purpose
AMoRE	phasing
CCP4	refinement
DENZO	data reduction
SCALEPACK	data scaling