2PHN | pdb_00002phn

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G9I	PDB entry 2G9I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	289	0.2 M Ammonium acetate, 0.1 M Sodium citrate, 25% PEG 5000 MME, 10 mM GDP, MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.367	α = 90
b = 98.367	β = 90
c = 94.347	γ = 90

Symmetry
Space Group	P 41 21 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	ADSC QUANTUM 315	mirrors	2006-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	1.35	40	98.7	0.055	22.3	8.2	99727	99727

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	1.35	1.37	97.9		0.49	4.69	7.5	4897

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	PDB entry 2G9I	1.35	40	99727	94754	4973	98.34	0.164	0.16179	0.1603	0.17	0.18997	0.2	RANDOM	15.446

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			0.41		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.187
r_dihedral_angle_4_deg	19.515
r_dihedral_angle_3_deg	12.472
r_dihedral_angle_1_deg	6.235
r_sphericity_free	5.961
r_scangle_it	3.703
r_sphericity_bonded	3.238
r_scbond_it	2.629
r_rigid_bond_restr	2.306
r_mcangle_it	2.009
r_angle_refined_deg	1.564
r_mcbond_it	1.493
r_angle_other_deg	0.955
r_mcbond_other	0.581
r_symmetry_vdw_other	0.333
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.226
r_symmetry_hbond_refined	0.218
r_nbd_other	0.206
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.092
r_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3809
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	98

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing