2AGG | pdb_00002agg

succinyl-AAPK-trypsin acyl-enzyme at 1.28 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AGE	PDB entry 2AGE with ligand and solvent removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.81	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.388	α = 90
b = 63.588	β = 90
c = 68.849	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2005-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.00000	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.28	46.63	96.27	0.075	0.075	9.3	3.1	59870	59870	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.35		51.9	0.475	0.475	1.7	2.2

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 2AGE with ligand and solvent removed	1.28	46.63	59869	59869	3027	96.27	0.125	0.125	0.124	0.13	0.158	0.16	inherited from PDB entry 2AGE	8.963

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]
0.83			-0.74		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.459
r_dihedral_angle_4_deg	20.84
r_sphericity_free	16.795
r_dihedral_angle_3_deg	10.63
r_sphericity_bonded	7.134
r_scangle_it	6.747
r_dihedral_angle_1_deg	6.679
r_scbond_it	5.464
r_rigid_bond_restr	5.198
r_mcangle_it	4.354
r_mcbond_it	3.455
r_mcbond_other	2.264
r_angle_refined_deg	1.742
r_angle_other_deg	0.933
r_nbd_refined	0.386
r_symmetry_vdw_other	0.325
r_symmetry_hbond_refined	0.283
r_nbd_other	0.264
r_xyhbond_nbd_refined	0.22
r_metal_ion_refined	0.143
r_chiral_restr	0.125
r_nbtor_other	0.094
r_symmetry_vdw_refined	0.032
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1648
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
EPMR	phasing
REFMAC	refinement
CCP4	data scaling