4ICS | pdb_00004ics

Crystal structure of PepS from Streptococcus pneumoniae in complex with a substrate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		2M MAGNESIUM SULFATE, PH 4.6, MICROBATCH, TEMPERATURE 295K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.365	α = 90
b = 126.365	β = 90
c = 139.328	γ = 90

Symmetry
Space Group	P 43 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	100	CCD	BRUKER PROTEUM 300			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6B		PAL/PLS	6B

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	1.97	50	99.6	0.083	42.06	9.3		75799

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	1.97	2.02	100		0.424	5.07	8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.97	41.2	75795	4012	99.6	0.227	0.225	0.21	0.257	0.24	RANDOM	29.58

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]
-0.06			-0.06		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.134
r_dihedral_angle_4_deg	21.441
r_dihedral_angle_3_deg	16.853
r_dihedral_angle_1_deg	6.55
r_scangle_it	4.769
r_scbond_it	3.066
r_angle_refined_deg	1.762
r_mcangle_it	1.655
r_mcbond_it	0.93
r_chiral_restr	0.142
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6364
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	42

Software

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