1XJQ

ADP Complex OF HUMAN PAPS SYNTHETASE 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X6V	PDB ENTRY 1X6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	290	1 mM ADP was soaked into native crystals (PDB ENTRY 1X6V) for one hour, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.5	α = 90
b = 82.5	β = 105
c = 133	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 ID14-4		ESRF	ID14-4

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	2.05	20	97.5	0.104	0.083	13.6	7.4		100470

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	2.05	2.1	89.5		0.609	0.741	2.48	5.8

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 ENTRY 1X6V	2.06	129.1	100470	92501	4869	96.56	0.17383	0.17135	0.18	0.22147	0.23	RANDOM	37.726

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]
1.6		1.22	0.77		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.54
r_scangle_it	3.694
r_mcangle_it	3.549
r_angle_refined_deg	2.474
r_scbond_it	2.411
r_mcbond_it	2.303
r_angle_other_deg	1.319
r_symmetry_hbond_refined	0.287
r_nbd_other	0.283
r_symmetry_vdw_other	0.249
r_nbd_refined	0.247
r_xyhbond_nbd_refined	0.235
r_symmetry_vdw_refined	0.2
r_chiral_restr	0.162
r_nbtor_other	0.107
r_bond_refined_d	0.034
r_bond_other_d	0.029
r_gen_planes_other	0.018
r_gen_planes_refined	0.016
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	9206
Nucleic Acid Atoms
Solvent Atoms	684
Heterogen Atoms	81

Software

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