2JAJ | pdb_00002jaj

DDAH1 complexed with L-257

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PART-REFINED DDAH1, IN-HOUSE COORDINATES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		289	PROTEIN: 20MG/ML IN 20MM TRIS-HCL PH 8.0, 150MM NACL, 1MM DTT. PRECIPITANT: 50MM TRIS-HCL PH 8.5, 150-300MM SODIUM ACETATE, 20-30% W/V PEG4000, 1MM DTT CO-CRYSTALLISED WITH 10MM LIGAND IN PRECIPITATING SOLUTION EXPT:SITTING DROPS UNDER MINERAL OIL AT 16DEG C

Crystal Properties
Matthews coefficient	Solvent content
2.46	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.849	α = 90
b = 46.914	β = 94.56
c = 147.612	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 CCD		2005-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	33.9	94.1	0.06	8.2	4.3		39147

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	2.11	86.8		0.15	2.2	4.4

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PART-REFINED DDAH1, IN-HOUSE COORDINATES	2	30	37137	2005	93.6	0.214	0.211	0.21	0.263	RANDOM	38.64

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]
2.58		-1.07	-0.16		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.074
r_dihedral_angle_4_deg	19.887
r_dihedral_angle_3_deg	15.098
r_dihedral_angle_1_deg	6.997
r_scangle_it	3.58
r_scbond_it	2.408
r_angle_refined_deg	1.669
r_mcangle_it	1.419
r_mcbond_it	0.967
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.224
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.113
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	4058
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing