1X6V | pdb_00001x6v

The crystal structure of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G8F	PDB ENTRIES 1G8F, 1D6J
experimental model	PDB	1D6J	PDB ENTRIES 1G8F, 1D6J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	285	91 mM sodium Citrate, 270 mM ammonium acetate, 12% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.21	α = 90
b = 82.55	β = 105.1
c = 133.6	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	CCD	ADSC QUANTUM 4		2003-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	30		0.069	11	3.6		159267		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	88		0.58	2.1	3.2

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 (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 WITH INITIAL MERCURY PHASES	THROUGHOUT	PDB ENTRIES 1G8F, 1D6J	1.75	129.1	165305	156571	8203	99.69	0.16789	0.1663	0.18	0.19811	0.21	RANDOM	24.273

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		0.24	1.4		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.913
r_scangle_it	4.932
r_scbond_it	3.07
r_mcangle_it	2.163
r_angle_refined_deg	1.805
r_angle_other_deg	1.48
r_mcbond_it	1.227
r_symmetry_vdw_other	0.299
r_symmetry_vdw_refined	0.272
r_nbd_other	0.26
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.227
r_symmetry_hbond_refined	0.224
r_chiral_restr	0.13
r_nbtor_other	0.088
r_bond_refined_d	0.021
r_gen_planes_other	0.014
r_gen_planes_refined	0.012
r_bond_other_d	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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9192
Nucleic Acid Atoms
Solvent Atoms	1091
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
X-GEN	data reduction
XDS	data scaling
XFIT	data reduction