1K9Y | pdb_00001k9y

The PAPase Hal2p complexed with magnesium ions and reaction products: AMP and inorganic phosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.693	α = 90
b = 45.075	β = 110.96
c = 71.794	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU RAXIS		1999-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	67.42	99.5			25897	25897

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.949	99.5

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 (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 1QGX	1.9	67.42	25847	25847	1306	99.43	0.15845	0.1559	0.17	0.20348	0.21	RANDOM	19.369

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]
-1.74		-0.42	1.47		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.566
r_dihedral_angle_1_deg	6.346
r_scangle_it	5.933
r_scbond_it	3.982
r_mcangle_it	2.656
r_angle_refined_deg	1.739
r_mcbond_it	1.711
r_angle_other_deg	0.83
r_symmetry_hbond_refined	0.349
r_symmetry_vdw_refined	0.247
r_symmetry_vdw_other	0.244
r_nbd_refined	0.235
r_nbd_other	0.219
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.113
r_bond_refined_d	0.015
r_metal_ion_refined	0.01
r_gen_planes_refined	0.006
r_xyhbond_nbd_other	0.006
r_gen_planes_other	0.002
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2727
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	35

Software

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