5G3Z

Crystal structure of adenylate kinase ancestor 3 with Zn, Mg and Ap5A bound

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 3 AND 10 MM MGAP5A IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (1.6 M SODIUM CITRATE TRIBASIC DEHYDRATE PH 6.5). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.617	α = 90
b = 77.435	β = 90
c = 38.628	γ = 90

Symmetry
Space Group	P 21 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		2014-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	1.89	77.43	100	0.18	8.6	6.7		16553		2.1

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	1.89	1.94	100		1.3	2.1	6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P3J	1.89	50.5	15482	1029	99.96	0.17862	0.17516	0.2325	RANDOM	20.952

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.479
r_dihedral_angle_3_deg	15.632
r_dihedral_angle_4_deg	13.467
r_dihedral_angle_1_deg	6.065
r_scbond_it	3.128
r_mcangle_it	2.737
r_angle_refined_deg	2.057
r_mcbond_it	1.795
r_mcbond_other	1.792
r_angle_other_deg	1.076
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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	1671
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
MOLREP	phasing