2HEU | pdb_00002heu

Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	30% (w/v) PEG 4000, 0.1M Tris.HCl, 0.05M CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.219	α = 90
b = 129.315	β = 94.21
c = 119.42	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	MARMOSAIC 225 mm CCD		2005-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9393	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	1.04	19.82	97.6	0.062	9.8	4.12	543433	543433			8.8

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)
	1.04	1.08	94.2		0.36	2.7	3.09	52441

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.04	19.82	543423	516098	27325	97.58	0.131	0.131	0.13	0.14	0.157	0.16	Extended from low resolution model	11.116

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]
-0.19		0.39	0.08		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.971
r_sphericity_free	15.103
r_dihedral_angle_3_deg	14.037
r_dihedral_angle_4_deg	9.09
r_dihedral_angle_1_deg	6.024
r_sphericity_bonded	5.939
r_scangle_it	5.732
r_angle_other_deg	4.247
r_scbond_it	4.239
r_mcbond_other	4.041
r_rigid_bond_restr	3.097
r_mcangle_it	3.057
r_angle_refined_deg	2.323
r_mcbond_it	2.263
r_symmetry_vdw_other	0.314
r_symmetry_hbond_refined	0.294
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.267
r_nbd_other	0.249
r_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.191
r_chiral_restr	0.14
r_nbtor_other	0.114
r_metal_ion_refined	0.077
r_bond_refined_d	0.029
r_gen_planes_other	0.015
r_gen_planes_refined	0.012
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10310
Nucleic Acid Atoms
Solvent Atoms	2552
Heterogen Atoms	13

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection