2J5Y | pdb_00002j5y

Crystal structure of the GA module from F.magna

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TF0	PDB ENTRY 1TF0, CHAIN B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		22-26% (W/V) PEG 3350, 50 MM POTASSIUM PHOSPHATE PH 7.5, 100 MM AMMONIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.784	α = 90
b = 58.068	β = 90.03
c = 40.57	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	MARRESEARCH	PT-COATED MIRRORS IN KB GEOMETRY	2005-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	1.4	40	94.4	0.07	11.7	2.5		22273		2

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	1.4	1.48	72.6		0.24	2.8	2.2

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 1TF0, CHAIN B	1.4	40.56	21101	1152	94.3	0.151	0.148	0.15	0.199	0.2	RANDOM	14.77

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]
0.34		-0.03	-0.32		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.002
r_dihedral_angle_3_deg	13.58
r_dihedral_angle_4_deg	7.325
r_scangle_it	6.545
r_scbond_it	5.017
r_dihedral_angle_1_deg	4.963
r_mcangle_it	3.749
r_mcbond_it	2.868
r_angle_refined_deg	1.61
r_nbtor_refined	0.315
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.223
r_xyhbond_nbd_refined	0.188
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
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	960
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms

Software

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