2HCR

crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and sulfate ion

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.15	293	0.1M citric acid, 1.3M ammonium sulfate, 0.02M sodium dihydrogen phosphate, 0.4M sodium chloride, 0.01M ATP, 0.01M cadmium chloride, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.236	α = 90
b = 170.236	β = 90
c = 61.82	γ = 120

Symmetry
Space Group	H 3

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 IV		2006-06-02	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)	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	2.2	25	97.1	0.074	7.9	5.59	33914	32945

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	2.2	2.28	96.8		0.359	2.1	5.67	3289

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H06	2.2	25	33914	32941	1672	97.13	0.208	0.205	0.205	0.254	RANDOM	36.369

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]
0.21	0.11		0.21		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.445
r_dihedral_angle_4_deg	17.364
r_dihedral_angle_3_deg	16.768
r_dihedral_angle_1_deg	5.393
r_rigid_bond_restr	2.956
r_sphericity_free	2.863
r_scangle_it	2.807
r_scbond_it	2.681
r_mcangle_it	1.628
r_sphericity_bonded	1.384
r_angle_refined_deg	1.163
r_mcbond_it	1.117
r_nbtor_refined	0.294
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4691
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	78

Software

Software
Software Name	Purpose
d*TREK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CNS	phasing