2R6V | pdb_00002r6v

Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii at 1.35 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	277	NANODROP, 0.2M Ammonium formate, 20.0% PEG 3350, No Buffer pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.2	α = 90
b = 46.2	β = 90
c = 267.59	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	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-07-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97939, 0.97910	SSRL	BL11-1

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	1.25	44.588	84.5	0.068	23.93	18.3		41184			15.957

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	1.25	1.29	28.2		0.318	3.2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	1.25	44.588	41182	2082	84.97	0.128	0.128	0.127	0.13	0.154	0.15	RANDOM	12.524

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]
0.58	0.29		0.58		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.349
r_dihedral_angle_4_deg	20.425
r_dihedral_angle_3_deg	12.533
r_sphericity_free	10.388
r_dihedral_angle_1_deg	6.341
r_scangle_it	5.458
r_sphericity_bonded	4.923
r_scbond_it	4.516
r_mcangle_it	3.552
r_mcbond_it	2.895
r_rigid_bond_restr	2.843
r_mcbond_other	2.077
r_angle_refined_deg	1.549
r_angle_other_deg	1.083
r_symmetry_vdw_refined	0.339
r_symmetry_vdw_other	0.276
r_nbd_refined	0.211
r_nbd_other	0.206
r_nbtor_refined	0.189
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.103
r_nbtor_other	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1444
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing