1PM4 | pdb_00001pm4

Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	293	Ammonium sulfate, PEG 200, sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.651	α = 90
b = 78.652	β = 91.97
c = 32.901	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 4		2002-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	1.071	SSRL	BL1-5

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	1.75	40	99.7	0.045	39.1	7.2	253851	253092

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)
	1.755	1.8	99.1		0.515	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.755	34.71	35113	33364	1749	99.3	0.18438	0.18438	0.18201	0.21	0.22926	RANDOM	18.498

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]
0.78		-0.9	0.07		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.836
r_scangle_it	4.2
r_scbond_it	2.833
r_mcangle_it	2.393
r_angle_refined_deg	1.897
r_mcbond_it	1.398
r_angle_other_deg	0.932
r_symmetry_vdw_other	0.308
r_nbd_other	0.263
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.126
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.12
r_nbtor_other	0.088
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2748
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing