1W6G | pdb_00001w6g

AGAO holoenzyme at 1.55 angstroms

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AV4	PDB ENTRY 1AV4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	THE CRYSTAL WAS GROWN BY HANGING DROP DIFFUSION AT 293K. THE RESERVOIR WAS 1.2M (NH4)2SO4, 12% DIOXANE, 0.1M MES PH6.5. THE DROP CONTAINED 1.5MICROLITER OF 11.7 MG/ML PROTEIN, 0.05M HEPES PH7.0, PLUS 1.5 MICROLITER OF RESERVOIR SOLUTION. A CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM., pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.836	α = 90
b = 63.243	β = 112.03
c = 91.982	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	100	IMAGE PLATE	MAR scanner 345 mm plate	58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUS MIRROR	2002-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	1.55	25.85	96	0.04	10.83	1.92		117993		-3	19.66

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	1.55	1.61	86.9		0.53	1.74	1.83

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1AV4	1.55	25.82	112062	5927	96.1	0.171	0.17	0.18	0.188	0.2	RANDOM	13.98

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]
-1.03		-0.07	2.47		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.313
r_scangle_it	5.771
r_scbond_it	3.861
r_mcangle_it	2.692
r_mcbond_it	1.792
r_angle_refined_deg	1.379
r_angle_other_deg	0.797
r_symmetry_vdw_other	0.315
r_nbd_other	0.252
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.118
r_symmetry_vdw_refined	0.113
r_chiral_restr	0.085
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4868
Nucleic Acid Atoms
Solvent Atoms	506
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing