4S2X | pdb_00004s2x

Structure of E. coli RppH bound to RNA and two magnesium ions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4S2W	PDB ENTRY 4S2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	crystal growth: 0.4 M ammonium sulfate, 12% PEG 3350, 10%glycerol. crystal soaking: 0.05 M MOPS-Na pH 7.0, 0.05 M ammonium sulfate, 0.05 M magnesium chloride, 15% PEG3350 and 25% pentaerythritol propoxylate 5/4 PO/OH, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.499	α = 90
b = 38.868	β = 100.13
c = 57.201	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	PIXEL	DECTRIS PILATUS 6M		2013-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	1.5	20	95.5	0.041		6.6	26827	26252	1	1

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	1.5	1.59	93		0.596	2.65	6.5	4066

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 (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	PDB ENTRY 4S2W	1.5	19.43	24889	24889	1310	95.52	0.19034	0.19034	0.18897	0.1849	0.21592	0.2116	RANDOM	29.221

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]
-0.85		-0.82	1.48		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.797
r_sphericity_free	28.598
r_dihedral_angle_4_deg	19.752
r_sphericity_bonded	18.384
r_dihedral_angle_3_deg	11.022
r_dihedral_angle_1_deg	6.36
r_rigid_bond_restr	2.741
r_angle_refined_deg	0.998
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1261
Nucleic Acid Atoms	54
Solvent Atoms	109
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CBASS	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing