Experiment: 3KAQ

Flavodoxin from D. desulfuricans (semireduced form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KAP	PDB ENTRY 3KAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	Reduced flavodoxin crystals were obtained directly from the oxidized ones. Since the original conditions of growth were at pH=5.0, the crystals were carefully transferred to 2.5M ammonium sulfate, pH=7.0, the pH required for the reduction to the semiquinone state. Within 10-15 min of 100mM sodium dithionite being slowly added, the crystal colour gradually changed from yellow to purple, corresponding to the stable semireduced state., VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.1	α = 90
b = 95.1	β = 90
c = 33.5	γ = 120

Symmetry
Space Group	P 32 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	MAR scanner 180 mm plate		1995-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.15	24	90.2	0.155		3.2	10220	9173

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)
	2.15	2.25	93.3		0.367		3.1

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3KAP	2.25	8	9112	8738			0.194	0.194	0.1989

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
x_dihedral_angle_d	26.06
x_angle_deg	2.981
x_improper_angle_d	2.38
x_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1067
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MAR345	data collection
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing