2QA9 | pdb_00002qa9

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	298	10 mg/mL SGPB in 10 mM MgCl2 0.7 M KH2PO4 pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.461	α = 90
b = 107.47	β = 90
c = 36.792	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 210		2003-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.954	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.18	20	98.3	0.071	12.4	3.6		56646

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.22	91.7		0.291	3.1	2.2	5212

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 1SGR	1.18	20	53726	2869	98.3	0.14727	0.1454	0.17	0.18204	0.2	RANDOM	7.577

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]
-0.75					0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.163
r_dihedral_angle_4_deg	20.659
r_sphericity_free	15.007
r_dihedral_angle_1_deg	14.368
r_dihedral_angle_3_deg	9.374
r_scangle_it	5.267
r_sphericity_bonded	4.846
r_scbond_it	4.563
r_mcangle_it	3.423
r_mcbond_it	2.973
r_rigid_bond_restr	2.512
r_angle_refined_deg	2.467
r_angle_other_deg	1.765
r_mcbond_other	1.543
r_symmetry_vdw_refined	0.339
r_symmetry_vdw_other	0.307
r_nbd_refined	0.232
r_nbd_other	0.221
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.195
r_nbtor_refined	0.184
r_chiral_restr	0.158
r_nbtor_other	0.095
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_bond_other_d	0.013
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1343
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing