3G5A | pdb_00003g5a

Crystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FMN and ATP analog AMPCPP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1 M Sodium acetate, pH 4.6, 8% (w/v) PEG 4000, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.831	α = 90
b = 81.753	β = 129.67
c = 136.698	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	113	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2007-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	1.95	50	96.4	0.088	11.517	2.5	123738	123738			19.4

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)
	1.95	2.02	97.1		0.447	2.094	2.5	12367

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	3FWK	1.95	35.07	123713	123713	6202	96.28	0.17845	0.178	0.175	0.18	0.236	0.24	RANDOM	19.286

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]
0.19		0.32	-0.16		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_3_deg	14.282
r_dihedral_angle_4_deg	13.015
r_dihedral_angle_1_deg	6.105
r_mcangle_it	1.963
r_scangle_it	1.835
r_angle_refined_deg	1.432
r_mcbond_it	1.274
r_scbond_it	1.24
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_3_deg	14.282
r_dihedral_angle_4_deg	13.015
r_dihedral_angle_1_deg	6.105
r_mcangle_it	1.963
r_scangle_it	1.835
r_angle_refined_deg	1.432
r_mcbond_it	1.274
r_scbond_it	1.24
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.094
r_metal_ion_refined	0.063
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14700
Nucleic Acid Atoms
Solvent Atoms	1790
Heterogen Atoms	397

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.