2CNU | pdb_00002cnu

Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A48	PDB ENTRY 1A48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.023	α = 90
b = 62.497	β = 90
c = 78.273	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH	MIRRORS	1997-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.05	24	94.4	0.05	24	4		131992			12

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	1.05	1.08	94.4		0.33	3	4

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 (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 1A48	1.05	23.97	125306	6644	100	0.134	0.132	0.15	0.159	0.17	RANDOM	13.06

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]
-0.5			-0.39		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.971
r_dihedral_angle_4_deg	19.971
r_dihedral_angle_1_deg	6.686
r_scangle_it	4.956
r_scbond_it	4.044
r_mcangle_it	2.988
r_mcbond_it	2.48
r_angle_refined_deg	2.242
r_angle_other_deg	2.056
r_nbd_refined	0.352
r_nbd_other	0.352
r_nbtor_refined	0.223
r_symmetry_hbond_refined	0.216
r_symmetry_vdw_other	0.199
r_symmetry_vdw_refined	0.188
r_chiral_restr	0.147
r_xyhbond_nbd_refined	0.103
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_nbtor_other
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_mcangle_other
r_scbond_other
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	2403
Nucleic Acid Atoms
Solvent Atoms	708
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing