Experiment: 1XP4

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NZ0	PDB entry 1NZ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293.15	potassium sodium tartrate, Tri-sodium citrate, sodium iodide, PEG 400, Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.608	α = 90
b = 120.839	β = 90
c = 177.076	γ = 90

Symmetry
Space Group	P 21 21 21

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		2002-05-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9792, 0.9794, 0.9393	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	65.84	99.9	0.102	0.102	12.7	5.4	47073	46098			31.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.98	100		0.279	0.279	4.7	5	7170

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	PDB entry 1NZ0	2.8	65.84	40041	37747	3309	99.8	0.237	0.237	0.2275	0.278	0.2672	RANDOM	28.9

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]
-8.29			17.69		-9.4

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.2
c_improper_angle_d	2.37
c_angle_deg	1.9
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10653
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	36

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing