2C10 | pdb_00002c10

The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	288	THE PROTEIN WAS CRYSTALLISED IN 0.1 M KBR, 0.1 M ACETATE PH 5, 38% PEG1000 AT 288 K.

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.236	α = 90
b = 130.236	β = 90
c = 221.529	γ = 90

Symmetry
Space Group	P 43

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		2004-05-14	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 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	2.5	51.6	100	0.1	13.8	5.2		126698		3.2	48

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	2.5	2.64	99.8		0.44	3.2	3.8

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 1KSI	2.5	20	124418	6243	98.2	0.204	0.204	0.2	0.252	0.21	RANDOM	37.62

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]
1.83			1.83		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.469
r_dihedral_angle_4_deg	19.747
r_dihedral_angle_3_deg	16.582
r_dihedral_angle_1_deg	6.42
r_scangle_it	2.278
r_scbond_it	1.343
r_angle_refined_deg	1.34
r_mcangle_it	0.922
r_mcbond_it	0.517
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.249
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	22300
Nucleic Acid Atoms
Solvent Atoms	563
Heterogen Atoms	607

Software

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