3CAM | pdb_00003cam

Crystal structure of the cold shock domain protein from Neisseria meningitidis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	0.8 M Sodium dihydrogen phosphate, 1.2 M di-potassium hydrogen phosphate, 100 mM Acetate pH 4.5, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.369	α = 90
b = 59.369	β = 90
c = 89.423	γ = 90

Symmetry
Space Group	P 41 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	MARMOSAIC 225 mm CCD		2006-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97900	ESRF	BM14

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	2.6	30	98.5	0.127	29.2	23.9		5271		-1.5

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	2.6	2.69	88.8		0.834	1.7	13.1	459

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	SAD	THROUGHOUT	2.6	30	4951	270	98.4	0.23646	0.23312	0.243	0.29663	0.2048	RANDOM	61.159

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]
-3.46			-3.46		6.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.476
r_dihedral_angle_3_deg	17.822
r_dihedral_angle_4_deg	15.191
r_scangle_it	9.741
r_scbond_it	7.333
r_mcangle_it	5.603
r_dihedral_angle_1_deg	5.359
r_mcbond_it	4.278
r_mcbond_other	1.167
r_angle_refined_deg	1.022
r_angle_other_deg	0.793
r_symmetry_hbond_refined	0.208
r_nbd_refined	0.184
r_nbtor_refined	0.183
r_symmetry_vdw_other	0.173
r_nbd_other	0.17
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.137
r_nbtor_other	0.084
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1014
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
SHELXE	model building