3CKM | pdb_00003ckm

LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	1.0M Li sulfate monohydrate, 2% W/V PEG 8000 and 0.05% BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.907	α = 90
b = 50.644	β = 106.73
c = 63.676	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	165	CCD	MARRESEARCH	Si(111)Monochromator	2004-10-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.97857,0.97843,0.96321	APS	5ID-B

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	1.35	47.1	99.4	0.044	12.2	3.14	144362	143557			14.73

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	1.35	1.4	99.3		0.428	2.8	3.1	14456

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	MAD	THROUGHOUT	1.35	38.95	73215	7201	99.39	0.16	0.157	0.1537	0.194	0.1901	RANDOM	14.197

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]
		0.01	-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.779
r_dihedral_angle_4_deg	14.455
r_dihedral_angle_3_deg	11.622
r_sphericity_free	7.731
r_dihedral_angle_1_deg	5.31
r_sphericity_bonded	5.238
r_scangle_it	5.018
r_scbond_it	3.53
r_mcangle_it	2.456
r_angle_other_deg	1.636
r_mcbond_it	1.616
r_rigid_bond_restr	1.598
r_angle_refined_deg	1.563
r_mcbond_other	0.898
r_bond_refined_d	0.015
r_chiral_restr	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2433
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	9

Software

Software
Software Name	Purpose
d*TREK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction