3MP9 | pdb_00003mp9

Structure of Streptococcal protein G B1 domain at pH 3.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PGA	PDB entry 1PGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3	290	Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.81	α = 90
b = 34.81	β = 90
c = 71.788	γ = 120

Symmetry
Space Group	P 32

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 QUANTUM 315	mirrors	2009-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

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	1.2	30.15	96	0.041	18.5	3.7	29246	27757			12.8

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	1.26	75		0.31	2.8	2.6	3333

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 (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 1PGA	1.2	30.15	29246	27757	1452	96.03	0.14971	0.14971	0.14825	0.15	0.18147	0.18	RANDOM	21.566

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]
0.36	0.18		0.36		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	33.536
r_scbond_it	30.701
r_dihedral_angle_2_deg	29.984
r_sphericity_free	29.082
r_rigid_bond_restr	23.658
r_sphericity_bonded	23.118
r_mcangle_it	14.04
r_mcbond_it	12.104
r_dihedral_angle_3_deg	11.52
r_dihedral_angle_1_deg	6.366
r_angle_refined_deg	1.215
r_nbtor_refined	0.303
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	958
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	6

Software

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